The people that began this movement considered themselves to be pure men of God, they thought that they were doing the right thing. The fact of the matter is that God gave men choice, free will. There are extremists in every area of life. Just look at the many terrorists bombing places in the name of their God, they believe that this is what he wants them to do, does it make it right? No.
Sure these me thought they were doing the right thing at the time, they were misguided, possibly the thought that they were doing this in the lords name made their rampage that much more powerful, but there were many other cruel things going on in that time. These acts were condoned by the pope, a mere man idolized by the catholic church, they took their orders from him (so they say), but that's just it, he was a man, not God.