I think it comes down to maintaining the illusion that religion somehow makes a moral difference. If, when tragic events happen, particularly involving the death of the young and innocent, why NOT blame atheists? After all if being religious and worshiping God is why people have morality, then surely immorality is a result of non-religious people. At least this would seem the logic used.
If religious leaders didn't blame atheists, their flocks might start to wonder how it is that people can be without God and still be moral. This would in a way invalidate the Christian faith. And lets not forget that in the Bible, when tragic events and natural disasters occur, it is almost inevitably because people are not following God, and God is punishing them. In a way it's nice to see Christians at least TRYING to have a worldview that is consistent with what the Bible actually says. It's refreshing in a way, and amusing as well since they are de facto admitting that God is an asshole.
If being godless had nothing to do with a lack of morality, the religious position would be pretty much pointless. The religious leaders and spokesheep have to maintain the illusion that religion somehow makes for a better, more moral society, or they would put themselves out of business. It also conveniently allows them to ignore the problem of evil, and instead blame evil on a lack of Godly followers, as if God didn't say that he creates evil too.
And let's face it: we are an ancient and convenient scapegoat. If religious people blame us for everything that goes wrong in society, it's a convenient distraction and excuse as to why the actual problems are not being solved. It gives them a reason to explain why God isn't helping us out. It's because those damn atheists! God won't cut us a break with hurricanes and shootings because he is punishing us for accepting immoral atheists into our society!
This conveniently allows them to ignore the issue of why God does not help in these cases, or indeed ever. It's just a handy excuse for God's failure to demonstrate his ability to shape the world in any way. It all helps to maintain the illusion that God is real, and is ANGRY with us for tolerating non-believers, who have made our society immoral, and our society is immoral BECAUSE we tolerate non-belief.
Because if non-belief doesn't make one automatically immoral, sheep might start to question why we need religion at all, and the donations and collection baskets would be less full, there would be less children to bully into compliance, less credulous ignorant people to take advantage of. Religion relies on maintenance of all of these things, and blaming lack of religion for the evils in the world is the only way they can try to validate belief in God in this day an age, because science has made all other aspects of religion laughable.
That's why they blame atheists. If they didn't, it would be an admission that God DOES NOT MAKE A DIFFERENCE.
EDIT: I would like to add that the reason, in my opinion, that we in America are having to put up with so much crap from religion right now is that religion is in its last gasp here in the US. It's a dying breed frantically trying to claw and tear its way through the opposition, as reason, education, science, and secular humanist values become more popular, and more and more people embrace a non-religious lifestyle. While a great many Americans may still identify as Christians, a majority of Americans also now support same sex marriage, equality for women, ending minority discrimination and other things that religion has always stood in the way of accomplishing. It's only to the extent that people have divorced themselves from traditional religious teachings that this is possible. It's only because people have had enough of Bible pounding lunatics spouting hate, blaming hurricanes on gays, saying rape is a gift from God, etc that we are starting to attempt to progress as a society and move towards joining the rest of the civilized world. The current super vocal religious fringe is so loud precisely because they are struggling to be heard and desperately need attention. And since they can't do any of the faith based stuff that would actually bring them positive attention, like healing amputees, they have to fan the flames of hate and intolerance, because it's all they have left.