Because people know that religion=power. If you haven't seen "Book of Eli", that movie explains it well. If you control the hope, you control the power. I think as a general rule, regardless of the religion, the people who follow it have pure intentions. However, there are people that recognize its power and try to take advantage of the followers of that religion. Crusades are one example. /The people behind them were corrupt, and took advantage of the followers of that religion to promote their own self interests. Im willing to bet many muslims agree that the "extremists" are not true followers of their religion either, and are just perverting it to progress their own self interest.
Religions are great, the people that try to manipulate them are the true evils.