Here is the catch, though many people will roll their eyes at it, the obvious is often the most over looked and the most ignored. Especially with an issue like the Middle-East, people want to ponder to therorize, and talk about social issues and types of government, the obvious answer is simply to obvious and simple to be taken into account and it tosses the whole idea of tolerance on its behind, which is a big no no. "Islam is a religion of peace!" how many time have you heard that one? It is very common retoric today. You simply don't diss other countries religions, Christianity is Europes religion, so it is fair game, but to diss any other religion is simply a blatant display of intolerance. That does not really bother me in this day and age of political correctness, but the problem with this way of thinking is that people decide it really is a religion of peace.
This is a hard one for me, I have quite a few friends who are Muslim, and I have long ago decided it would be prudent to avoid discussing religion with them, though it comes up from time to time. Most of my Muslim friends never read their Qur'an, the one friend I have who does read his Qur'an sometimes makes me nearly pee my pants on account of some of the comments he makes. He says them half jokingly, but he still manages to scare the shit out of me sometimes.
I have studied the Bible extensively, and I have studied the Qu'ran a little, I admit I have not studied the Qu'ran as much as I should, and I intend to get back into it more sooner or later.
Okay, back to the obvious answer I mentioned in the first paragraph. The religion of Christianity is based on the New Testament of the Bible, the religion of Islam is based on the Qur'an. If we want to understand the difference between the two religions, let's look at their texts.
No matter what someone believes, you will find nuts and extremists, bad things have been done in the name of Christianity, as well as in the name of science and evolution. You have people who do bad things for all sorts of reasons. Science does not teach us to do these things, neither does Christianity*. The problem with the Qur'an is that it does support this kind of behavior. It does promote hate. It is not a religion of peace or tolerance, you would be very hard pressed to make even a poor attempt at an argument saying that it is. Their behavior is not a product of their culture, so much as that their culture is a product of their religion. This is not a very popular take on the situation, so I would not be surprised if I get some pretty harsh backlash on this one, but I would encourage anyone who disagrees with me to either send off for a free Qur'an or pick one up at the local library and do some reading. It will be an extremely enlightening experience.
*the Bible never even mentions abortion, let alone calls Christians to kill abortionist, it never says to hate homosexuals, only that homosexuality is a sin, the Bible teaches us to love everyone. It condemns liars, theives and prostitutes as heavily as it does gays, yet those are the kind of people Jesus chose to hang around. If you read through the new testament you'll find that it is all about tolerance. When "Christians" behave intolerantly they are not even obeying their own religious text.