Because the perpetrator of the Chapel Hill shootings was an atheist, atheism is being blamed as the ideological motivator of the murders. It seems illogical to blame a philosophy which is only defined by a lack of belief in gods. There are neo-Nazi Social Darwinists and pacifistic Buddhists who are atheists. There are Ayn Randian Objectivists and radical communists who are atheists. And yes, there are atheists who kill their fellow human beings in cold blood simply because of a hatred of their religious belief or skin colour. Conversely, there are atheists across the world, such as in Saudi Arabia, who are killed, tortured and persecuted because of their apostasy; as are the personally religious advocates of political secularism. There atheists who are great scientists and humanitarians, and there are atheists who advocate all bigotries and quackeries imaginable (other than, perhaps, religious creationism). Bill Maher, for example, advocates anti-vaccination quackery, while Christopher Hitchens was a shill for neoconservatism.
Mentioning Nazism, it is evident that Hitler was anti-religious but ruthlessly exploited Christian belief for political gain (and incidentally viewed Islam as a more practical vessel for Nazism). Holocaust architect Himmler, in contrast, pursued the extermination of Jewry as part of a holy war within an esoteric belief system which promoted the God-given divinity of Germanic Aryans. Similarly, the agnostic Dutch far-right demogauge Geert Wilders aligns himself with Christian fundamentalists and fascistic Zionists, in a xenophobia-charged culture war against Muslims, in the name of secular humanism. Wilders and his ilk manipulate atrocities such as 9/11 to smear the majority Muslim population, the very kind of propaganda exercise the reactionary anti-atheists have engaged in with these shootings.
The anti-atheists in this case will thus retort that this is a matter of the influence of New Atheism; a belief system within itself they say, nominally headed by high priests like Dawkins and Hitchens (presumably since 2006), homogeneously habituated by white, heterosexual western males who promote crypto-racial and cultural supremacy in the name of so-called enlightenment. No doubt such prejudices should be challenged regardless of ideological mediums they project themselves through, whether this be by those self-justified by theological belief or otherwise. (And as stated in the aforementioned paragraph, both are keen to collaborate to further their bigoted ends).
The central falsehoods of such arguments is that they depend upon the presumption of an actually organized and ideological unity between atheists, which even within the narrow western parameters they refer to there is none. The closest demonstrable thing to philosophical belief system among secularists is humanism: which stands for the human rights of all people, including the right to life, freethought and religious freedom. These are values which all reasonably minded people, in opposition to all repression and willful ignorance whether religious or atheistic, can stand for.