How does a religion become evil?
Well-intentioned people can do things and justify behavior that contradicts what's at the very heart of their religious tradition, and it can descend into cruel and violent behavior.
One example is a belief in absolute truth. People who believe they have God in their pocket and know what God wants for them have proven time and again that they're capable of doing anything because it's not their will but God's will being carried out. You see this most obviously in a suicide bomber-someone who is convinced he or she knows what God wants, and can end up doing the most horrific things to innocent people.
Another example is blind obedience to a leader. When people become so convinced of a particular person or charismatic leader that they blindly will follow that person, it can lead to Jim Jones and Jonestown. It can lead to the Buddhist group Aum Shinrikyo in Tokyo in 1995 that released sarin gas in the Tokyo subway system. There's a pattern in sects, and also in local churches, where power is concentrated in too few hands with not enough checks and balances. And you can have a charismatic leader who gets out of control.
One of the scariest examples is the belief that the end justifies any means. Every religion is predicated on the notion that something in the world is terribly wrong. If we weren't ignorant we wouldn't need the Buddha to enlighten us, and if we weren't sinful we wouldn't need Jesus to save us, and if we weren't forgetful we wouldn't need Muhammad to guide us. The presupposition that something is wrong is premised on rectifying that wrong, overcoming obstacles, and moving toward a more hopeful future or meaningful end, whether that's heaven or nirvana or whatever. And often that has a component of making life more just and peaceful. That's normal.
The problem is when people become convinced they know the route to the peaceable kingdom and they are God's agents to make it happen. And here is where you get groups of extremist Jews whose messianic mission leads them to tunnel under the Dome of the Rock and try to blow it up in order to facilitate the building of the Third Temple. Or Christian fundamentalist groups who long for Armageddon to the point that they will support violent extremists trying to destroy the Dome of the Rock. Now, pious Orthodox Jews pray for the coming of the Messiah and the Third Temple, which they believe God will bring down from heaven. But that's a very different thing from saying, "I'm going to give God a helping hand and blow up some buildings in the process."
And this behavior is dangerous in a place like Israel and Palestine. You have millions of Christians fixated on Armageddon theology. They spend a great deal of time watching TV preachers, picking apart Bible verses, looking at headlines in the news, patching together pieces of information to create a sort of image that "Jesus is coming on Tuesday." But when I read the New Testament it's pretty clear Jesus says nothing like, "On Judgment Day how much of your puzzle did you piece together?" He says, "When I was hungry, did you give me something to eat, and when I was thirsty did you give me something to drink?" The mandate of following Christ involves reaching out to people in need, and peacemaking. Whether Jesus comes next Tuesday or in a thousand years is really God's business.
Even worse, there are many well-intentioned Christians who actively oppose any kind of reconciliation among Israelis and Palestinians because it's theologically counterintuitive to them. They say, "Why would you work for peace when we know Armageddon is about to occur?" In their theology Israel is part of God's plan. This is one of the most dangerous things because you put that over against 50 million copies of the Left Behind series, which makes good reading, but a lot of people gobble this up as though it's God's truth.