I disagree immensely that a fundamentalist version of a religion or cultural system has nothing to do with the religion itself. Fundamentalism is just the strict maintenance of ancient or fundamental doctrines, and if those doctrines (which, mind you, are right there in both the holy book of the religion as well as its entire history) lead to terrible human rights abuses, then it is the fault of the religion being fundamentally adhered to. In many ways, you can best understand a religion by looking at its fundamentalists because they give you the most basic, traditional and strict look at what that religion teaches.
If a religious text or tradition can be turned into a death machine simply by people actually doing all the things it commands, then that certainly does reflect on the merits of that religion. A good example of this is Jainism. Their "fundamentalists" do exist and they manifest that traditionalist viewpoint by not leaving home after nightfall so that they can be sure they don't step on any bugs. You won't find radical Jain fundamentalists blowing up buildings because that prescription of violence simply doesn't exist in their religious philosophy; no amount of strict adherence or fundamentalism could find such abusive behavior in their religion. On the other hand, it's really fucking easy to see justification for such violence in the Quran, for example. So if the fundamentalists, aka the people doing what the religion actually says you should do, are killing civilians and murdering women, then I think that shows at the very least that such behaviors are easy to justify with the Holy Book of whatever religion you're looking at.