What came to popularity in the "new atheist" writings of Richard Dawkins, Christopher Hitchens, and Sam Harris, has now become an internet atheist slogan; viz., that there is an inherent relationship between religion, intolerance, and violence. But that is false.
Consider atheist David Steele, e.g., who reminds his fellow atheists that the "history of the past one hundred years shows us that atheistic ideologies can sanctify more and bigger atrocities than Christianity or Islam ever did." (Steele, Atheism Explained: From Folly to Philosophy, xi) (See also "David Berlinski, Evil & Religion, and Pinker's "Shockingly Happy Picture"" - Berlinski is also an atheist.)
I recently received a review copy of Religion in Today's World: Global Issues, Sociological Perspectives (ed. Melissa Wilcox). In "The Association of 'Religion' with Violence: Reflections on a Modern Trope," Richard King writes:
"The mainstream discourse on 'religion and violence' and the emphasis that has been placed upon this as a recurring problem of human history is the secularist equivalent of a 'lone gunman theory'. By focusing one's attention upon the apparently intolerant, dogmatic and socially disharmonious aspects of purportedly indentifiable entities known as 'the religions', our attention is distracted from asking deeper, structural questions about violence as a condition of modern, 'everyday' life and about the involvement of human beings in the performance of such violence - whether grounded in so-called 'secular' or 'religious' forms of life." (496)
I feel certain King is correct on this. Any internet-atheist claim that religion is the root of violence is unstudied and sophomoric.