"As 14 year-old Malala Yousafzai sat on a bus in the grounds of her school in Pakistan's Swat Valley, a gunman shot her in the head. After proudly claiming responsibility, the Taliban told the world that the teenage education activist's work represented "a new chapter of obscenity, and we have to finish this chapter". The "obscenity" was the education of girls.
The Taliban felt no shame. They know that what they have done is right because their god tells them so. Gods have been used to justify almost any cruelty, from burning heretics and stoning adulterers to crucifying Jesus himself.
On the other side of the world, Anders Behring Breivik slaughtered 77 Norwegians. Breivik seems to have seen his murderous spree as a way of getting rid of Muslims, yet his 1,500-page manifesto revealed, at best, a weak attachment to religious belief. To Breivik, Christianity seems important mainly because he sees it as white. Breivik, like the devoutly religious Taliban, also appears to feel no shame.
The men who flew planes into buildings on 9/11, the Pakistanis who went on a murderous rampage in Mumbai and the Bali bombers, all killed as many people as they could in the name of their religion. Breivik did it in the name of his race. Timothy McVeigh, who killed 168 people and wounded 800, hated the government. All saw their mass murder as a political act of protest and all felt justified.
Atheists like Mao or Pol Pot have murdered millions in the name of political totalitarianism. Hitler used a quasi-mystical racist philosophy to exploit the ancient hatred of the Jews by Christians. I heard somewhere (I've never been able to discover where) that terrorism occurs when you combine a sense of military and economic inferiority with a sense of moral superiority. Religion is very good at conferring a sense of moral superiority on its followers.
Indeed, while the religious have murdered throughout history in the name of their god, I've been unable to find any evidence of atheists killing anyone in the name of atheism. Atheists are no more or less capable of evil than anyone else, but it seems that murder, particularly mass murder and war, is a sin of commission. In other words, human beings are generally only prepared to fight and kill in the name of something. It can be a god, but it can also be a political philosophy – like nazism or communism. Many fight for patriotism: for country, tribe or race. Some kill because they're psychologically disturbed, but none – so far – in the name of atheism.
So, while I don't agree that only religion causes conflict, I'd argue that all mass murder and war are fought in the name of a bigger-than-self philosophy or idea.
Atheism, simply lack of belief in a god, has not yet proved compelling enough to motivate murder. So far no one has gone into a crowded public space and blown themselves up while shouting, "No god is great!".