I don't know if Christians have any greater record of inquisitions and witch hunts than anyone else does. Christians invariably think that Christianity matters, and that what it has to say is important and worth spreading. But you need something more than that to get witch hunts etc. You need the idea that this end justifies the means used to accomplish it, and that it is appropriate to use the weapons of power to get people to believe the right thing. Most Christians today, I think would say that a forced belief in Christianity isn't real one, and that such actions on behalf of Christianity are inappropriate and self-defeating. The people who brought the idea of a free and democratic society to the Western were mostly Christians. Any democratic society needs religious freedom to survive. For political reasons, autocratic governments pursue religious (or non-religious) uniformity. Democratic ones ordinarily tolerate opposing religious views. Islam is somewhat of a different case, because Islam, is rooted in the idea that the government should be implementing it. That's why it's so hard to get a democracy going in an Islamic country.
Now Christian autocrats have pursued Christian uniformity, and often pursued Catholic or Protestant uniformity. Atheist autocrats have also pursued atheist uniformity, as in the case of the League of the Militant Godless in Russia. The way this is prevented is not by supporting or opposing religion, it is by saying the governments should stay out of the business of enforcing uniformity in matters of religion.
People will sometimes say atheism is a non-belief, not a belief, but in the minds of many this non-belief matters. Some, like Dawkins, think that society will either progress or regress depending on whether or not we are successful in ridding ourselves of religion, which they consider to be irrational superstition. So, if you have the power to use force to help eliminate religion, or to force it on others, would you use it? If you were given Tolkien's One Ring, and could use it to make everyone religious or everyone nonreligious would you use it? If religion or lack of it matters, and most of us on both sides think it does, then it is always possible for anyone to "use the ring" to compel assent, if the power to do so is present.