To be fair, a lot more people have been murdered for not worshiping the right god than have been murdered by a non-theist for worshiping any god. Hell, there are two religions that can probably "win" this all by themselves.
To be fair, for most of history, non-theists were not in a position to kill religious folks for being religious, but there are plenty of examples from the 20th century to show that it can and will happen. Just because followers of two religions have had more opportunities to be assholes doesn't mean followers of those religions are more likely to be assholes. Assholery seems to be an equal opportunity fault for both theists and non-theists.