Several points:

1. This is a silly, if not also a thoroughly common, argument. If the negative actions of any and all theists reflect badly upon all theists, all forms of religion and all religionists then it follows that the negative actions of any and all atheists reflect badly upon all atheists, all forms of irreligion and all irreligionists. This logical fallacy is called "Guilt by Association."

2. Communism is definitely a religion as the Catholic Church has claimed for more than a century. It's an atheistic religion. It's a religion created by atheists, celebrated by atheists and defended by atheists. It comes with its own prophets and prophecies, sacred items, soteriology, hierotopy, pseudo-spirituality, pseudo-morality, pilgrimages, temples, theophany, soteriology, cultic practices, sacred texts and exegetical commentary.

3. Even if we were to ignore the obvious crimes against humanity that atheists involved in the global communist movement in the past century have committed, we can condemn all atheists and atheism simply by examining the one million dead at the hands of "rational," "enlightened" atheist French Revolutionaries. Historians call the Vendean Martyrs in March 1793 the modern-era's first genocide. The atheist French Revolutionary Army ordered the conscription of 300,000 citizens of Vendée. Having already had all of their churches suppressed and their bishops slaughtered, this infuriated the populace which rose up in "The Catholic Army." In response, the Revolutionary Army massacred 6,000 Vendée prisoners, many of them women, children and the elderly, after the battle of Savenay. In addition, 3,000 Vendée women were drowned at Pont-au-Baux. In addition, 5,000 Vendée priests, elderly, women and children were tied in groups in barges and drowned in the Loire River at Nantes. By July, AD 1796, nearly 500,000 Vendean Catholics were killed. All of these theists were killed at the hands of atheists. Considering this was the first cry of "public" atheism—as opposed to individuals who simply didn't believe in God throughout Christian history—atheists have yet to explain why "compassionate" and "rational" atheists' hands are so murderously bloody.

4. If the above statement were true, it might make the atheist case unassailable. However, anyone who has read a newspaper at any time between the 17th and 21st centuries knows this to be untrue. This is one of the atheists' fondest lies. I'm not sure that the person about to be executed by a Marxist or Maoist atheist is assuaged in the knowledge that his evil, merciless executioner isn't killing him because he's an atheist but rather because he believes in an atheist philosophy and only coincidently doesn't believe in God. Multiply this by all 152 million dead at the hands of atheists in the 20th and 21st century—a carnage which has yet to abate—makes the above claim perfectly worthless. In addition, we have more than sufficient proof that atheists killed in the name of atheism as in the case of the Soviet Union's Society of the Militant Godless, Mao Zedong's Red Guard, the Enlightenment's Reign of Terror, Abimael Guzmán's Shining Path, atheist Napoleon's wars and Plutarco Elias Calles democide of Mexican Catholics during the Cristero Wars.

5. Atheists who make nonsensical, ahistorical and misological claims such as this one, prove they've never truly examined their own community's behavior under the microscope as they enjoy doing with us. Consider instead those who have died in the name of atheistic philosophies such as marxism, socialism, communism, maoism, Nazism, fascism, totalitarianism, libertarianism, monopolistic capitalism, robber barronism, industrialization, secularism, jingoism, anarchism, social darwinism, eugenics, malthusianism, messianic scientism, nihilism, anti-humanist terrorism, individualism, narcissism, physicalism, materialism, consumerism, modernism, postmodernism, nietzscheism, Marquis de Sade's sadism, (i.e., sadistic murders) moral relativism, hedonism, radical feminism, (i.e., abortions, infanticide, suicide, false claims of rape) radical environmentalism, (i.e., ecological terrorism) Anton LaVey's satanism, (i.e., ritual murders) and the "Law of Attraction." (i.e., the deaths, including suicides, caused by Peter Popoff, Sylvia Browne and other gurus") All of these atheistic philosophies have resulted in the deaths of countless hundreds of millions of human beings. In comparison, the deaths caused by religion seem almost quaint and insignificant.

6. But even if we were to never mention any of the dark secret murders of the atheist community ever again, an important question remains begging to be begged: Why is it that no one has ever been helped anyone in the name of atheism? There has never been anyone who has ever given a crust of bread or a drop of water or a stitch of clothing to anyone in the name of atheism. (Richard Dawkins admits in his The God Delusion that it's "easier to herd cats than to get atheists to cooperate each other." This goes a long way in explaining why atheists refuse to cooperate with each other and form charitable concerns. Christians easily cooperate with each other otherwise hospitals and schools would never get built.) 

If this is incorrect, where are the army of atheists humanitarian traipsing about Africa and Asia giving hope to the poor and disadvantaged? Certainly none of the famous atheist polemicists have ever done so. Christopher Hitchens was asked on multiply occasions if he or other atheists who similarly had a poor opinion of St. Mother Teresa have actually gone to India and rolled up their sleeves to bathe lepers. I've asked many atheists including P.Z. Myers, Patricia Churchland and Christopher Hitchens and none have responded in the positive. Madalyn O'Hair never mentioned having done so. Mao and Stalin were busy killing tens of millions of their compatriots by engineering famines in their respective countries so it's hard to imagine they also helped poor people. When I volunteered at Mother Teresa's street clinics in Calcutta, I never met an atheist doing the same work but I routinely met Catholics doing so.

Regardless of their obviously false claim that atheists have dutifully avoided murdering anyone, it's a rather worthless commentary if a community has done nothing positive for humanity. Most humans have never killed anyone but this hardly makes those most people saints or Nobel Peace Prize material. (Mother Teresa was both.) It would be a sad epigraph on an atheist's tombstone if it read, "He never helped a single individual, but at least he never killed anyone except as a result of his indifference and apathy." Most prison convicts and related sociopaths have similarly not killed anyone but the fact that they're in prison proves they've disregarded the rights and needs of others. Only atheists put humanitarians in prison as in the case of the Soviet Union and Post-Revolutionary China, North Korea, Cuba, Cambodia and Viêt Nam.

7. Further, the fact that many atheists are glib or gratified at the horror of mass murders committed by their fellow atheists goes a long way in proving they are mere contrarians. One can't glibly disregard the suffering of others while ignoring the fact that others (i.e., Catholics) are working towards alleviating suffering in the world and throughout it all, lying about their good works—that's requires a special kind of evil which is hopefully extremely rare in this world.

These philosophies and the horrors they generated aside, fundamentalist atheists should rather worry about the kind of people they hope to attract to their community when they mock religion. Truly compassionate, generous, gentle, kind and forgiving people won't be attracted to a group that mocks others. I've been a Catholic for a long time and I have never heard the word "atheism" or "atheist" ever mentioned in church. Having been an atheist prior to reverting to Catholicism, I can assure you that that community is obsessed by the Church finding themselves incapable, or unwilling, of discussing anything other than the most recent reason for hating us. They never talk about the wonders and glories of atheism or the joy that it engenders in their hearts. They never raise virtuous atheists as models for themselves and their children. They never organize themselves to help the unfortunate. It's because they can't and simply don't want to.

Frankly, after a couple of years, I simply couldn't take it anymore. I left atheism behind because it was snarky, sniping and moribund reveling in its bitterness and denial. It's amazing anyone psychologically and spiritually survives the wholesale rejection of hope, logic and reality as they cherry pick data to uphold their opinions. Or, maybe, it's because God has a special place in His heart for atheists. As G.K. Chesterton points out, God even sustains atheists in their disbelief.