It appears that the man who gunned down three Muslim students at UNC-Chapel Hill was a Proggy Atheist.The police are now saying that the murder was over a parking dispute.
Look, that may have been the trigger, but that was not the powder, if you receive my meaning. You settle parking disputes with passive-aggressive notes and towings. You don’t shoot people.
It reminds me of Christopher Hitchens’ rebuttal to the contention that Communism counts as atheist violence. To Hitchens, Stalin created an ersatz religion in the Soviet Union, with himself as a kind of god, so all the crimes of Russian Communism were in fact, caused by religion. The people of Russia simply exchanged the Russian Orthodox Church for the Communist Party.
It’s a clever argument, but it hides a horrible weakness: if a thoroughly athest-materialist philosophy like Communism can create a religion as murderous as any theist, then what is the point of atheism? If it does not insulate us from the violence that the righteous meet out against heretics, what value does it have?
Not that anyone will answer. The current play is to keep the Tea Party meme in operation. Whatever demonizes the Other.
Content Blues 
1. Atheism doesn’t advocate anything other than that there are no gods, so comparisons to violence inspired by religious texts are specious. (You don’t explicitly make this comparison, but others have.)
2. The value of atheism is that it frees us from one source of nonsense and violence that plagues human culture. Unfortunately, there are plenty of others.
3. People kill each other over things much more trivial than parking disputes:
In June John Richard Nosler was convicted of shooting Armando Marra to death in 1990 because Marra was insufficiently grateful for the loaf of bread Nosler had brought him. According to Nosler’s statement, read at the trial, “(Marra) rudely said, ‘Well, give it to me.’ This was the comment that actually pushed me over the edge.” Nosler had shot Marra four times, then said to himself, “Well, I can’t stop now,” and fired again.
http://www.chicagoreader.com/chicago/news-of-the-weird/Content?oid=880074
In Cleveland in April Henrietta Page, 46, was charged with stabbing her husband to death as a result of an argument about whether the dog could sit on the couch.
http://www.chicagoreader.com/chicago/news-of-the-weird/Content?oid=880361
Montique Ramon Brown, 18, surrendered to police in Richmond, Virginia, in March and confessed that he had shot a man to death at 12:05 AM on January 1. He told police he did it because he wanted to commit Richmond’s first murder of 1992.
http://www.chicagoreader.com/chicago/news-of-the-weird/Content?oid=879669
Thanks for the comment. Where I think you go wrong is where a lot of people go wrong, in assuming that violence done in the name of any belief system is somehow rooted in that belief system, i.e. religious violence only exists because incredulous sheeple persist in positing the supernatural.
Thus, you can say “Atheism advocates nothing other than there are no gods.” Correct. And Christianity advocates nothing other than the Son of God died for our sins. Violence does not lie in either of those advocacies. The violence comes later, when people decide that a) their belief is the only correct one and b) it is actively harmful to believe otherwise. That one-two punch morally authorizes the use of force. Which is why communists were prepared to kill millions in the name of dialectical materialism. In fact, like Godfrey de Buillon and ISIS, they were proud of their commitment to violence.
I can’t say that the New Atheists have reached that point yet. But, given the way Dawkins talks about religious instruction being comparable to child abuse, I think it’s safe to say they’re not running away from it. YMMV.
Your other point, about how people kill for things smaller than parking violations, is entirely just.