I agree with you that there is no such thing as good or bad germs.  They are incapable of moral choices therefore they can neither be good or bad.  They just are, but think not! - My apologies to Descartes. 

I would also support the idea that it is unnecessary to wipe all microbes from our lives, and the clot of anti-bacterial soaps, lotions, wipes are a marketing ploy that profits from ignorance and fear.   A 1:20 dilution of bleach is a perfect disinfectant to use around the house, nothing more is needed.  The careful use of antibiotics has greatly improved the quality or our lives and well as our overall survival and longevity.  Unfortunately our ability to target only 1 specific microbe does not exist and we must make due with the relatively broad action of our current drugs.  

You are falling into the naturalistic fallacy by believing that just because germs are fulfilling their natural functions we should not kill them.  Just because something is natural, it does not make it ‘good.’  Even germs have chemical defense mechanisms against other germs, and use various means to limit their growth, kill them or out-compete them for resources.   So, if these germs are causing us harm of have the potential to cause harm we would be negligent if we did not take action.

The war on bacteria/viruses is a war that we are winning; diseases which would have previously killed us or would have required extended recovery periods can now be effectively treated.    Something like Hansen’s disease (ie, Leprosy a term which is falling out of use) which has plagued humanity since the beginning can easily be treated with the right drugs.
 
You are also wrong in believing that only if you have a weak immune system will germs cause harm.  Like in poisons, the dosage is also a factor, as is the method of delivery.   So you can be exposed (ex. Ingest / inject) to a few bacteria without any problem but the same bacteria in large amounts will overwhelm any defenses and cause disease.    The idea of beefing up the immune system is also wrong headed.   A proper working immune system does not need ‘beefing up’, many autoimmune diseases are a result of an immune system in overdrive.   Boosting the immune system is not desirable, not unless you happen to have an immunodeficiency.

Germs do make you sick, but it is also true most are benign and have no effect on health.   Though if you think you can prove that the germ theory of diseases is false, please forward you findings to the nearest science journal.  You will be hailed as one of the greatest scientists of our generation.   

Bearing in mind that some choose to discard history, here is a bit relevant to your post. Keeping in mind that some are also averse to input beyond a paragraph or so at one sitting,  the below reference unfortunately is, well, that, but it's nothing personal. Sometimes the opportunity for insight or enlightenment requires a bit more effort than a drive-thru approach and a willingness to consider things others already did  further back than, say, yesterday, yesteryear and perhaps even century ago and more.    

http://www.ahealedplanet.net/medicine.htm#germ

Pasteur’s Germ Theory, Vaccines and Alternate Paradigms

Semmelweis eventually enlarged his sanitation theory to include any decaying matter as infectious.  He died before Pasteur developed his germ theory of disease.  Béchamp’s work supported Semmelweis’ theory that any rotting material can induce infection.  Rotting, put more scientifically, is fermentation, or the digestive processes of microscopic organisms.  Béchamp ended his The Blood and its Third Anatomical Element with,

“The living being, filled with microzymas, carries in himself the elements essential for life, for disease, for death and for destruction.  And that this variety in results may not too much surprise us, the processes are the same.  Our cellules [cells – Ed.], it is a matter of constant observation, are being continually destroyed by means of a fermentation very analogous to that which follows death.  Penetrating into the heart of these phenomena we might really say, were it not for the offensiveness of the expression, that we are constantly rotting!”[214]

It is a testament to Béchamp’s keen talent that he documented the microzyman world with his day’s microscopes.  With bacterial and fungal forms (and recall Rife’s cancer virus) as morphic stages of microzyman/somatidian/bionic/endobiontic evolution, there is a direct connection between degenerative and infectious disease. 

Pasteur’s germ theory sees the body is a victim to organisms that attack from outside the body.  Microzyman theory sees the destruction as coming from within.  Béchamp was not alone in his theorizing about “harmful” organisms being created by the disease, not the other way around.  Pasteur’s friend Claude Bernard thought the same way, as eventually even Rudolf Virchow did.  Bernard theorized that the environment the germs lived in was all-important, not the germ.  The “harmful” germs were only reacting to a dangerous environment.  Legend even has it that Pasteur acknowledged the same thing on his death bed, saying that Bernard was right, the “the microbe is nothing, the terrain everything.”[215]

Béchamp theorized that the so-called germs in the air were only the floating microzymas of dead organisms, and would initiate fermentation and turn to bacteria if given a favorable medium.  They would not cause disease, in Béchamp’s opinion.  Lister eventually abandoned Pasteur’s air-germ theory and stopped spraying carbolic acid into the air, and eventually stated that only germs from non-air sources were harmful.  From that time forward, Lister only sterilized surgical implements, wounds and dressings, which led to today’s sterile surgical procedures. 

Pasteurization, antibiotics and vaccination derive directly from Pasteur’s germ theory.  Pasteurization involves subjecting fluids such as milk, beer and orange juice to high heat, to kill microorganisms that can lead to illness.  According to microzyman theory, Pasteurization stops the fermentation process by halting the microzyman nutritive process.  Pasteurization also destroys all enzymes and most vitamins.  The nutritional value of food is greatly reduced through pasteurization.  Pasteurization is the ancestor of today’s irradiation.  Those processes are attempting to overcome filth and putrefaction with scorched-earth-style destruction.  Far healthier is a clean product that has not been subjected to destructive heat or radiation.  Then there would not be any need for such practices.  Even better is adopting a live food diet, eliminating those processed foods.  

Antibiotic theory comes directly from the germ theory, where powerful drugs and organisms kill those invading germs.  According to microzyman theory, the deadly germs are usually not of the invading variety, but are local germs reacting to a diseased environment, taking a new shape in response, in the germ’s struggle for survival.  That is similar to Naessens’ theory of how healthy cells become pirates when their environment is poor, and diseases such as cancer result.

The antibiotic era began in 1928 with the discovery of penicillin.  In the 1940s, penicillin became publicly known and immediately became the Wonder Drug.  Penicillin, however, was another scorched-earth treatment.  It killed all bacteria, not just the “bad guys.”  According to microzyman theory, something such as penicillin did not make the diseased “terrain” healthy, it just wiped out all bacteria in the environment, or more precisely, a morphic stage of a pleomorphic life cycle.  The other stages still existed.  The bacteria also adapted to the new scourge, as they have adapted to change for billions of years. 

In 1952, staphylococcus infections were about 100% curable with penicillin; today that number is less than 5%.  New antibiotics are continually invented to overcome the developing resistance of bacteria.  The weakening and destruction of the immune system is one outcome of antibiotic use.  Antibiotic use is nearly universal in the American population, and new “super bugs” appear every year, so more powerful antibiotics are developed.  Now, hospitals are the realm of those super bugs, and about 80,000 Americans die each year due to infection that they acquired in hospitals, infections that will not respond to antibiotics.  At the rate it is going, the antibiotic age will be over soon, as the “bad” bacteria will have adapted to all the antibiotics that have been thrown at them.  The effect on the immune systems of those who have taken antibiotics has been immense, especially as Americans take antibiotics these days for the slightest sniffles.  The price for short-term relief will likely be long-term disaster, and Naessens’ work demonstrates what other problems collapsing immune systems can lead to.  The antibiotic age is a form of arms race, in typical masculine fashion, always seeking ways to make the perfect weapon.  Arms races never have a happy ending. 

Vaccination is another outcome of Pasteur’s germ theory.  Pasteur was not the first vaccinator, as Edward Jenner and others had the idea for smallpox much earlier, but Pasteur provided the theoretical basis, and he was the first great commercializer of the process.  His anthrax and rabies vaccinations were two early instances of the commercialization of vaccination.  As with fluoridation, assessing vaccine effectiveness is a numbers game.   In Hume’s book, she deals at length with the effectiveness of vaccination, especially Pasteur’s.  Before Pasteur pursued his vaccines, smallpox vaccination became mandatory in England, and the numbers are illuminating.  In 1840, smallpox vaccines became free in England and Wales.  In 1853, the vaccine became compulsory.  In 1867, those who did not submit to vaccination were prosecuted. The deaths in England and Wales from smallpox are presented for the pertinent years.[216]

Epidemic years	England and Wales smallpox deaths
1857-1859	14,244
1863-1865	20,059
1870-1872	44,840

In addition, smallpox mortality increases in vaccinated populations.  While the U.S. fatality rate from smallpox was less than 3% of cases around 1900, in the far more vaccinated U.S. Army in the Philippines, the fatality rate was more than 25%.[217]  The highest death rate in the Philippines during the smallpox epidemic of a century ago was in Manila, with a fatality rate of 65%, and Manila was the most heavily vaccinated place in the Philippines.  Vaccination makes the disease more deadly when contracted.  George Bernard Shaw remarked on the statistical fraud that took place in England in trying to make vaccination appear more successful than it was. 

The standard history books fail to mention that Pasteur’s early experiments with his vaccine were disastrous.  Pasteur’s plagiarized vaccine was used on thousands of sheep in Southern Russia.  The vaccine was administered to 4564 sheep, and 3696 died almost immediately from the vaccine.[218]  Pasteur had to pay for all the animals he killed with his “preventive.”  The numbers show similar success with Pasteur’s rabies vaccine.  He may have even invented a new disease with that vaccine.  Time and again, the actual effects of vaccination show something very different from unqualified success.  A chapter of Hume’s book is devoted to the vaccination lessons of World War I.  Disease caused nearly as many casualties during the disaster at Gallipoli as those dead and wounded in battle, with heavily inoculated troops.  The grand finale of World War I was an “influenza” epidemic that swept the world in 1918-1919, beginning at a U.S. military base and killing probably at least 25 million people and crippling my grandfather, who was in the trenches during World War I.  They thought he was dead, and put him in a makeshift morgue with other soldiers.  He awoke days later in the charnel house, and nearby soldiers were spooked to watch a man crawl out of there.  Rheumatoid arthritis accompanied his illness, which crippled him.