Do they both kill bacteria, the good and the bad, therefore are harmful for the flora?

Pharmaceutical antibiotics generally kill the flora.  As for herbs it depends on the herb.  Some herbs such as the berberine herbs (goldenseal, barberry, Oregon grape root, coptis, etc.) will kill the flora.  But other antiseptic herbs such as clove, pau d' arco, chaparral, etc. will not kill the flora.  There can be various reasons for this.  For example, some herbs are absorbed long before they would have a chance to reach the flora.  Some herbs are specific t their targets depending on how they are excreted.  For example,  eucalyptus is specific to the respiratory passages since it is excreted through the lungs.  Uva ursi does not become antiseptic until it reaches the kidneys where the aglycones are converted in to antiseptic hydroquinones.  Then there are gram positive and gram negative bacteria, and different herbs may only target one or both types.  Most of the beneficial flora are comprised of gram negative bacteria.  An herb targeting only gram positive bacteria would have little effect on the flora.  And keep in mind that the fibers from herbs are prebiotic and therefore help feed the flora.

Why the herbs such as pau d'arco and chaparrel that we take to try to kill a bunch of bateria and virus are not considered as harmful to the flora? Or may be they are. Then when we take this herbs, should we also need to take prebiotics and probiotics? I am a little confused on this issue, please, enlighten me.

Again it all depends on the chemistry of the particular herb as to whether or not they will pose a problem to the flora.