Since religion can be a factor in the irrational actions of some people, this is no doubt a timely subject. Two things come to mind when I think about this, though.
First of all, it's my understanding that the purpose of religion is only there to point the way, but is not the way itself. It doesn't matter to me if you're religious or not, the way I look at it is your relationship to ultimate reality, whether you believe in God, gods or nature. So for that matter, any system of belief such as the ones we have from the various religion's sacred writings are only descriptions. So in a way, you shouldn't take it too seriously or too literally, in that it is not the whole story, only a general outline at best.
This leads to the other point I thought of, which is the matter of interpretation. Aside from the fact that it's hard to understand the original language etc, there is the tendancy to find support for one's own views from these writings. Obviously, it's a matter of taking things out of context in that case, because you're only looking for something to support your own views. (which is a type of behavior that is not limited to religious people) In that case you can't blame the religion for the actions of the individuals, if they are indeed misapplying the scriptures or misrepresenting the doctrines which they profess to believe in. They're really promoting their own ideas in that case. If we are going to criticize the religion which these people claim to follow, lets look at the religion itself. But as far as blame goes, lets look at the individuals who are actually responsible for these acts, rather than condemning entire categories of people.