Excellent points. Here's the difference though. The most atrocious deeds performed in the name of Christ were performed in violation of Christ's word. The crusades (or at least the brutality which occurred during them), the inquisition, the salem witch trials, all of these are violations of scripture.
The most atrocious deeds done in the name of islam are perfectly in accordance with, and commanded by the koran. WTC, the actions of the taliban, palestinian homicide bombings, all perfect examples of adherence to koranic commands. The islamic is commanded to fight with the unbeliever near to them.
So we have on one hand a religion whose main command is to love God and love your neighbor. (Christianity)
On the other hand we have a religion whose command is to fear God and subjugate or kill your neighbor. (islam)
Which would you expect to live peacebly and which would you expect would have to be eradicated for peace to exist?