The fact is that while religious wars have been fought for centuries, militant atheism has slaughtered more people than religious zealots ever have. The greatest mass murders in history have been committed not by Christians but by Communists Joseph Stalin and Mao Tse Tung. More than 100 million have died at the hands of these militant atheists since the early 20th century.
First - the argument is used to oppose the assertion that religion has been at the root of many of history's darkest moments, which is meaningless because it is like comparing the Green River Killer to the Night Stalker. Both were heinous murders, both are equally guilty. One killing more than the other does not absolve either of the crime. So you can say, atheism has been a theme in the murder of millions, just as religion has been a theme in the murder of millions.
Second - Stalin, Mao, and Hitler were in the service of a larger calling - politics. Communism and Fascism suffer no competition. Religion was suppressed in the service of politics. Millions died in the name of ego and political philosophy, not atheism.
Third - religion was the state for centuries. A long hard struggle against religion resulted in successful secular governments who champion freedom. The United States and France are great examples. The long bloody history of the Catholic church and Islam are undebatable.
In the final analysis, it is true believers who are guilty. The true believer in religion, or the true believers in political theory, or the true believers in atheism for that matter. Any choice, when taken to an extreme, leads to intolerance of opposing views, and ultimately violent suppression.