While atheists are quite understandably relucant to embrace "their" responsiblity for the mass murders committed by their brethren, what they consistently fail to understand is that pinning the responsibility on the atheistic murderer is not about implying that the average atheist today is inclined to commit mass murder, but rather demonstrating the complete absudity of the often made case that historical crimes committed by those of vaguely similar beliefs somehow justify advocating legal or social restrictions on individuals who have not committed any such crimes.
Atheists aren't the only ones guilty of such guilt associations. Medieval Christians certainly did so, and some of the more foolish Jews do the same thing today, forgetting that if it is right to judge today's Christians for the historical crimes of medieval Christians who persecuted Jews, then those medieval Christians were entirely justified in persecuting medieval Jews for the crimes of anceint Jews who persecuted Christians. Responsibility must either be assigned individually or collectively. If the former, then no Christian today can be held responsible for the Crusades, no atheist today can be held responsible for the Holocaust, and no Jew today can be held responsible for killing of Jesus Christ or any of his followers. If the latter, then Christians, atheists, and Jews are all justified in engaging in a war of all against all. I feel that such a war is immoral and unjustifyable, and so chose to believe that responsiblity must be assigned individually and that all (atheists, Christians, Muslims, Jews, etc.) are capable of doing horrible things as well as benevolent things.
But with regards to the mass slaughters of the previous century, there is simply no way to escape the established fact that individual atheists have been among mankind's very worst killers. This doesn't mean that the average atheist is any more likely to be homicidally inclined than anyone else. It does, however, cast serious doubt on the common atheist assertion that a godless society will unquestionably be a peaceful one. The significant question has never been if atheism causes political leaders to kill in large quantities, it is why political leaders who happen to be atheist have been inordinately inclined to kill in large quantities.
The answer is probably to be found in the fact that atheists who have committed great historical crimes are almost exclusively atheists with utopian visions of restructuring human society. Ayn Rand atheists aren't exactly known for attempting to violently restructure societal order. This is why atheists like Sam Harris, Christopher Hitchens, and Michel Onfray are far more dangerous than people like Benedict XVI or even Richard Dawkins.