The biggest problem with Islam itself is how intricately tied to politics it is. Islam is both a religion and a political system.
We can talk all day about how other religions (especially Christianity) have been tied to politics, but there's nothing in the doctrines themselves that advocate taking control of politics. Islam has from the very start been intensely political. Ideally, Muslims should live in a country ruled by Sharia law, which is enforced by a Caliph. Obviously, saying that every Muslim wants this is moronic and blatantly untrue. But that doesn't change how it was established by Muhammad himself. From the beginning, Islam has been a “total way of life.” It has provided guidance in every sphere of life, from individual cleanliness, rules of trade, to the structure and politics of society. In other words, it doesn't just provide guidance for one's personal life and affairs, but rather society as a whole. I can't think of any other major religion that's like this.
Personally, I believe that Islamic extremism won't die down (mind you, not disappear entirely) until Islam itself establishes a separation between mosque and state. Christianity became much more benign and more focused on Jesus' actual teachings after the rise of secularism. But the problem is that Jesus never actually said anything about Christians needing to attain power in the first place; quite the opposite, actually (what with the whole "the meek shall inherit the earth" thing and all). Muhammad himself was an intensely political figure and constantly emphasized how important it was for Muslims to establish their own laws. He also constantly asserted the supremacy of Muslims and how they needed to overtake the kaffirs (non-believers) and impose Islamic order.
Anyone who says that politics don't play an important role in Islam is either delusional or a liar.
Again, I don't think all Muslims are evil terrorists who want to murder Christians and drink their blood. In fact, most Muslims you'll talk to have no desire to live in a theocracy and love democracy just like the rest of us. But I think that Islam itself is in serious need for a reformation and is long overdue for one.