I think the basic problem with most Monotheistic institutions, including the Judaic, Christian, and Islamic religons, is the idea that "God" (in whatever form) is on your side. Therefore, all other religons and their followers are wrong and evil. If "God" is on your side, and you are fighting for "him", there is no crime that you can commit in "his" name.
You're not killing, you're "purifying", "cleansing", or (even more cynically)"bring 'God' to the masses". Anybody who resists you is resisting "God", and therefore evil in the extreme. Executing them becomes more than a mere nesessity, it is a duty to the Almighty himself. Rape, murder, pillage, all are forgiven, because you are doing the "Lord's Work". And if you die, don't worry. You become a "martyr" to the cause. And we'll kill even more people in your name. Plus, you'll get a fast pass to "Heaven" and your ultimate reward.
The really sad part of this all is that neither the Torah, the Bible, nor the Qhu'ran, advocate or excuse this type of thinking or behavior. In fact, all unanimously denouce it as evil. However, RELIGOUS LEADERS are the people who are twisting and defiling the very things they claim to uphold, usually to expand their power among people. After all, they're "selected/blessed by 'God' ", and therefore able to correctly 'interpret' his words and meanings.
The problem isn't with religon, per se. The problem comes from religous organizations. One person shouting out that 'somethings wrong' isn't dangerous. But when authority figures, especially those espoused to be to be leaders of their communities religous beliefs, start 'preaching' hate and intolerance of others.. well now we see the backlash this generates in others who become the victims of those views.
Don't get me wrong, because I in no way support or agree with those who are willing to trade liberty and justice for security and a false sense of peace. But, the only way to truly 'win' this type of attack, is to refuse to change at the others behest. Every time we ltrade away our rights for some false sense of security, they win. It simply encourages them to do bigger and more damaging attacks, because they can make us change, which is their goal.