The problems that surround the "religious violence" claim have to do with the level of generality at which the issue is addressed. For example, one of my complaints with Dawkins is that he claims that 9/11 gave him a reason to start a militant crusade on behalf of atheism as opposed to religion. My objection to him bears considerable similarity to my objection to the claim by Donald Trump that Muslims should be excluded from coming to America because some of them are terrorists. The problem is that while bin Laden and I are both theists, I am more than willing to operate within an open society, and he wants to use political power and even terror to advance what he takes to be the cause of Islam. I object to Trump's statements because in order to get from Islam to the terrorist ideology you have to take about three right turns, and there are plenty of Muslims who exist quite peaceably in an open society. I think there is a difference between Christianity and Islam in that Christianity has no statecraft in its founding documents, (all the Bible says about government is "Render unto Caesar"), while the Qur'an does purport to tell you what to do with government.
Religion can lead to violence since religions typically assert what is most important to those who believe them. But religion does not guarantee how much a believer will care whether others believe as they do. In fact, I've seen atheists care a whole heck of a lot more about other people believing as they do than I do as a Christian. I am also inclined to concur with Christian thinkers from Lactantius to Locke and the Christians who moved Europe toward democratic government and instituted religious freedom, in that I maintain that meaningful religious devotion should be free and voluntary, and there is something inherently self-defeating about forcing religious truth on others. If one thinks one's views in matters of religion are true, then to some extent we want others to agree with us, but there are ethical and unethical ways of getting others to agree with us. (Ridicule, as a method of persuasion, seems to me to be a form of violence. Sticks and stones can break our bones, but it is just false to say words can never hurt us).
It is sometimes asserted that religious believers have more motivation for coercive conduct than secularists, since believers think there are eternal consequences of believing or not believing, while secularists do not recognize such eternal consequences. I don't buy this. Some atheists say we are on the cusp of history, that whether we renounce faith or not will determine whether we will progress or regress as a culture. If you really believe that, then it's going to be tempting to advance the cause of atheism any which way you can. Some forms of atheist advocacy, they become widespread, may convince some people, but it may at the same time prompt religionists to protect their culture by homeschooling their kids or sending them to Christian schools, and it will also prompt a resurgence of the Religious Right. What we will get is more cultural fragmentation than we have already, and I think that will be unfortunate.