Many times atheists will point out the Salem Witch Trials, the Inquisition, and ISIS. Theists, in turn, will bring up Mao, Stalin, and others. I think this line of reasoning is a failure on both sides aisle. What matters is what logically follows from a specific view point. People can do harm for a variety of reasons. If we are going to pin horrors specifically on either atheism or theism we need the harm to logically follow from one of them.
Bare with me, I actually don’t think harm logically follows from either atheism or theism. Atheism simply means the lack of belief in god(s); while, theism simply means the belief in a personal deity. The terms atheism and theism tells one very little about what motivates a person, and there is no doctrine or dogma that goes along with either of these views. It is thus necessary to look further into what motivates these people. Is the theist, who is causing harm, a Christian, Muslim, or other? Does Christianity or Islam justify this harm? I will let you make up your own mind. What is the atheist, who causes harm, motivated by? Are they part of ideological worldview like say communism? Does their ideological worldview justify the harm they are committing? I will, once again, let the readers make up their own mind.
The point neither theism nor atheism in and of themselves can be responsible for atrocities. Nothing in these terms justifies bad or good behavior. What matters are worldviews that justify atrocities, and I will leave it to the reader to decide which religions or worldviews justify atrocities.