I am with Thomas Jefferson when it comes to religion: "it does me no injury for my neighbor to say there are twenty gods or no God. It neither picks my pocket nor breaks my leg." This libertarian strain leads me to get slightly upset when people blame any other religious group for any reason. My friends, knowing I am easily needled, quote Christopher Hitchens (of God is Not Great fame) to me whenever they can. Borrowing from C.S. Lewis' The Problem of Pain, I came up with the following argument, which gently straddles the line between proselytizing and confirming faith as a private matter.
1. If you agree guilt is innate, explain where it comes from? At such a young age, we've all felt guilt. Assuming socialization at that young of an age could not have played a part, where did it come from, if not God or something we cannot understand and therefore name "God"?
2. Agree that humanity is not omnipotent. Okay. Agree that humanity will always be subject to the unknown, which will nevertheless have real effects on a person's life. Okay. If you believe in cause and effect, the unknown that causes effects has to come from somewhere. Religion assigns a name to that unknown and calls it "God." To not believe in God is to reject the concept of the unknown.
One way to escape that conclusion is to say "Yes, at some point, humanity will be able to explain everything or will evolve to be able to explain everything." That is not a humble explanation.
So the atheist must post this scenario: God-believers are wrong and humble, and atheists are not humble but right and can be omnipotent. Therefore, the main difference under an atheist's view between believers and non-believers is believers are predisposed to humility and possibly stupidity. I agreed with this position my friend advocated. I'd rather live in a world where people are humble and wrong than arrogant and right. That division, at the end of the day, seems to be one difference between believers and nonbelievers. Just my two cents from a former atheist (just like C.S. Lewis).
As for calling particular religions harmful, the New York Times's Lindsey O'Rourke reminds us that terrorism crosses all lines. See A27, August 2, 2008, "Blaming Islamic fundamentalism [for female terrorism] is also wrongheaded. More than 85 percent of female suicide terrorists since 1981 committed their attacks on behalf of secular organizations; many grew up in Christian and Hindu families...The founder of Hamas claimed 'A woman martyr is problematic for Muslim society. A man who recruits a woman is breaking Islamic law."' And, "95 percent of female suicide attacks occurred within the context of a military campaign against foreign occupying forces, suggesting that, at a macro level, the main strategic logic is to create or maintain territorial sovereignty for their ethnic group" (e.g. Tamil Tigers--see an overlooked but incredible Indian film called A Peck on the Cheek for more).
Of course, Hamas' anti-Semitic comments contradict the Quran's Sura 2:256: "There shall be no compulsion in religion." Just goes to show you can bring a man to the book, but you can't make him understand it.