Fear and loathing and militant atheism
It's always interesting to watch the "separation of church and state" crowd go weak in the knees before Islam, bending over backward to accommodate it after treating Judeo-Christian faith like a virus for decades. Obviously, a big part of this stems from the atheist-progressive belief that radical Muslims will respond to religious insults by killing them. These people are cowardly bullies, not the champions of principle they pretend to be. They wage war against Christmas displays because it's easy. They crave the polite disapproval of the folks who want to put up Nativity displays. They love to portray those people as hateful extremist bigots who might be prone to violence, but they know they aren't really prone to violence.
There's also the enduring left-wing narrative of America the Evil, which holds Christian faith as an accessory to oppression. In the great liberal psychosis of interlocking power narratives, Muslims are still classified as Oppressed People of Color, although they're right on the edge of being downgraded to Hapless Bystanders. But Christianity is a big part of the "dead white male slaveowners with powdered wigs" construct that socialism has been at war against for the better part of a century. They calculate no political gain from picking a fight with Islam, especially given the likely consequences. Also, such a conflict would come dangerously close to a concession that Chimpy McHitlerburton and his neocon sidekicks have a point. Why, the Wrong People are pushing anti-sharia-law ordinances even as we speak!
I'm convinced that deep in the faculty lounges and liberal think-tank meetings, there's one more reason for the astounding difference in the way atheist socialists react to Christianity and Islam. I think they've noticed that Islam is rather more compatible with centralized political power. It's proven useful to all sorts of dictatorships, while troublesome Judeo-Christian tradition led to all that Constitutional stuff, with its talk about rights endowed by a Creator who is forever above the power of the State. There's all manner of hypocrisy to mock, but there are also some ice-cold tactical decisions being made by the devotees of total politics.
None of which has anything to do with well-meaning atheists, agnostics, or Muslims, who have precisely as much right to their beliefs, and the respectful consideration of their fellow Americans, as everyone else. And I do mean precisely.