Republican bombers are not motivated by religion, that's just the excuse. It's a political struggle and always has been. If you knew anything at all about the place, you would know that.
Islamic fundamentalists are just using Islam as an excuse to. All the religions that spawned out of that region (Judaism, Christianity and Islam) all have some pretty wacky stuff in their that most of the religious people tend to ignore.
It's not the system of beliefs per se it's how it's used. Similar to communism. The original teachings of Marx are beautiful, utopian ideals, but when applied under the soviet system did the opposite of what the intent was.