Hi Chris, its regretful to hear that opinion. I can't vouch for the Bible as I don't know it sufficiently well in order to defend, but as a Muslim I can guarantee that any "honest" reading of the Quran does not legitimise any attacks on any people simply for not believing in the same thing, and quite the opposite actually supports them and within reason allows other religious communities to rule via their own laws.

What the Quran does legitimise is conventional war or conflict to end oppression. That oppression does not have to be committed against Muslims, and can be done on behalf of any group that is wrongly victimised. Neither side of that conventional conflict actually has to be "Muslim", as it is a general statement of how conflict, as bad as it is should be run in order to promote an eventual peace that supports everyone.

Quranic law on conflict is fairly well documented and is fairly easy to understand and includes the following:

Innocents should never be killed. In fact, there is a complete ban on the murder of any woman, child or elderly person in Islam. That means that the only possible "lawful" killing that can be committed under Sharia law would be that against an adult male combatant in a time of war or under the death penalty if a nation chooses to use it (and of which there is a very limited amount of crimes that Islam allows the death penalty to be used; namely murder and rape).

The contents of any persons belongings taken after death in battle/war is food and weapons. That is, personal belongings of anyone killed must remain on the body until it can be delivered to the next of kin; a ban on looting of others personal possessions. There is a default system in Sharia law on how possessions are divided up to the next of kin if no will has been drawn up or witnessed prior to the persons death.

Prisoners of War must be well fed and treated, even if they are a pain in the ass. The worst thing that someone in possession of a POW can do to them is bind them in order to prevent escape or violence. Torture is regarded as unacceptable. There are also rules regarding POW's transfer back to their nations origin. POW's can only be traded for POW counterparts that that nation has captured among your men, or food. That is it. The preferable case is to simply release POW's as a good will gesture without necessarily anything in return.

Furthermore, and this will be the last point I make, there is also a command to accept peace if it is offered by the other side. While Islam (and I don't know how this is for other religions) accept that conflicts and war do happen, these sets of rules are designed to ensure the safety of all innocent bystanders and POWs and to end the conflict as soon as possible.

Whether or not Muslims follow these rules is plain to see within current events, the answer is obviously not all of them; which is a deep shame and leads the the tragic deaths of innocent people and a perception that Islam discriminates against non-Muslims which is untrue.

I hope this has been informative to anyone looking for knowledge on the subject. If you do not accept Islamic legitimacy, which your all free to do; remember these rules would then have had to be written by some human sometime in the 7th century or prior; long before international law (which arguably doesn't go as far as some of this).