I don't think there's a lot I can add to the discussion that has already taken place here, but I'll give my 2p anyway.
It's very helpful when considering the question asked by the OP to attempt to differentiate between religion and religious extremism, since they are very different philosophies with very different motivations. Religious extremism can't exist without the framework of religion of course, but then neither can pseudo-political extremism (e.g. Anders Breivik) exist without politics. Nor can insanity exist without sanity...
More importantly it is key to note that any form of extremism must be considered in light of the mental state of the perpetrator. There are very few cases in which a person or group commit crimes under the banner of extremism without some kind of mental issue, whether that be delusion, paranoid schizophrenia, depression or shock - amongst many others.
On the whole, although I am an atheist I am happy to co-exist with normal religious folk as long as they go about their business and I can go about mine with minimal disruption. But I always have to question how things would be if religion and mass delusion had never evolved in the human race. I understand of course that this would never have been possible, as the capabilities of the human mind evolved far more rapidly than our understanding of the fixed laws of the universe, or the subjective, flexible framework of morality and eudaimonia. Religion crept in to answer those questions a long time ago and has never left us despite the fact that I truly believe it is no longer relevant, particularly in the civilised world.
I have often questioned where the human race would have ended up had this inevitable twist not occurred. Even as atheists we are forced to accept that our moral framework is largely based upon millennia of religious dominance, and we are quite often sold the theory that without religion the world would be a far more brutish place. However, I strongly disagree with this concept based on what we can observe in the natural world. Other animals are capable of living together largely harmoniously in order to maximise their individual "success". I believe that in a parallel universe where religion had never dictated morality the human race would still be thriving and successful, possibly even more so. Of course there would always be conflict with or without religion, but if you take away the artificial segregation of religion it is one less flashpoint to worry about.