I'm not sure why some atheist think they hold a higher moral ground based on their belief of, no God. Perhaps it is because they are not aware of past and even recent historical facts that atheist under the right circumstances can be just as ruthless as any Christian crusader or modern Muslim terrorist. In February of this year an atheist belonging to what was thought to be a defunct terror group that espouses atheism turned himself into "Mince" as Higgs Bosoms likes to put it, in front of an American Turkish embassy. 

http://www.washingtonpost.com/blogs/worldviews/wp/2013/02/01/turkey-bombing-what-is-the-dhkpc-terrorist-group/
Now, I know what the atheist here will say, "No, he's a communist not an atheist." And to that I would say, he is both. Lets revisit a very famous Communist who's ideas killed an estimated 80,000,000 people, Vladimir Ilyich Ulyanov. Here are few things he said and wrote.
"Atheism is the natural and inseparable part of Communism"
"Down with religion and long live atheism; the dissemination of atheist views is our chief task"
"Our program necessarily includes the propaganda of atheism"
But, I know you're thinking "Who gives a flying fox fart about some dude named Vladimir Ilyich Ulyanov". Otherwise know as Lenin. No Lenin didn't do all the killing all by his lonesome, he had to have parters, like Stalin, Mao, Pol Pot, Nicolae Ceau and of course Kim Jung Il. 
Just as Christianity got dangerous when it politicised and now Islam as it poloticises so did and still does atheism as it politicises.