If they don't control most of the nodes in-between they can control all the exit nodes they want. If you connect though 3 Tor nodes, as soon as one of them is not controlled by them they likely can't identify you.
That's not to say that they don't control most of the nodes, and your traffic likely goes through NSA nodes exclusively
Here's my hypothesis. People have little contact to Muslims and the way Islam is being usually practiced. Thus people's opinion of Islam is heavily influenced by the worst shit and stereotypes. With Christianity most people have friends or relatives that are "moderate" christians or whatever. So the worst versions of Christianity are less present.