Few people have been killed "in the name of atheism." Millions were killed in the name of Communism. Hundreds of thousands were killed in the name of Christ.
In all cases, the killing was by fanatics. They each suffer their own particular delusions, but they are all fanatics.
more have been killed in the last 100 years in the name of athiesm than in all of the past 2000 years in the name of "God".
Yes, however, there were a lot more people alive in the past 100 years then there were (say) 1,000 years ago. Also, the means to kill people in large numbers (technology) are much more advanced now then they were prior to 100 years ago.
One hears figures that something like 1/3 of the population of Germany was killed due to the 30 Years War (between Protestants and Catholics)....whereas nowhere near 1/3 of the population of Germany or any other country was killed as a result of WWI, or WWII. If you can wipe out 1/3 of a country's population with pre-industrial weapons (plus disease and starvation following in the wake of the armies), what would such a war have been like with modern weapons? As to communist regimes, some of them have murdered large portions of their own population, but figures vary wildly as to proportion - perhaps as high as 1/3, mostly due to starvation. Would these figures have been lower if they had been religious fanatics? Even if the religious fanatics thought they were doing the world a favor by fighting Satan in the form of unbelievers? Even witch hunters thought they were doing the witch a favor by offering him/her a chance to repent and save his/her soul before being burnt.
An atheist may behave worse because he does not believe in an afterlife or eternal reward/punishment.....or he may behave better, because this life is all there is, and we have to take actions which will make the world a better place in the future. A religious person may behave better because he believes in an afterlife and eternal rewards and punishments...or he may behave worse because he believes that this world is essentially unreal and temporary, and that it is better to destroy and kill the "evil" rather than risking his own eternal soul or the souls of others (the "kill them all, God will know his own" way of looking at things).
It really all boils down to exactly how one choses to interpet one's belief system: atheism is as much a belief system as any religion, and there is no such thing as an atheist orthodoxy (unlike religious orthodoxy). All things being equal, I am more nervous of a religous fanatic with nukes than I am of communist atheists with nukes, since the atheist's self interest is to preserve the things of this world, not forsake them for the "truly real" world of the spirit.