Think Progress says the whole thing is old whine in new bottles:

The right-wing’s “War on Christmas” conspiracy rhetoric isn’t at all new, though the scapegoats have changed some.

In the 1921 screed “The International Jew: The World’s Foremost Problem,” automaker and notorious anti-Semite Henry Ford observed that “most people had a hard time finding Christmas cards that indicated in any way that Christmas commemorated Someone’s Birth.” He noted menacingly, “Now, all this begins with the designers of the cards.”

Later, the Soviet Union and the United Nations were fingered for plotting to undermine Christmas. A 1959 John Birch Society pamphlet stated, “One of the techniques now being applied by the Reds to weaken the pillar of religion in our country is the drive to take Christ out of Christmas — to denude the event of its religious meaning.” The writer sounded the alarm: “Department stores throughout the country are to utilize UN symbols and emblems as Christmas decorations.”

As Salon.com’s Michelle Goldberg writes, “To compare today’s ‘war on Christmas’ demagogues to Henry Ford is not to call them anti-Semites.” Yet Jews are not entirely absent from their campaign.

Fox’s Bill O’Reilly to Jewish caller: “You have a predominantly Christian nation. … And you don’t wanna hear about it? Come on, [caller] — if you are really offended, you gotta go to Israel.”

Fox’s John Gibson: “The wagers of this war on Christmas are a cabal of secularists, so-called humanists, trial lawyers, cultural relativists, and liberal, guilt-wracked Christians — not just Jewish people.”

More importantly, those who warn of a “War on Christmas” these days promote a conspiracy theory “that repeatedly crops up in America,” in which the “scheme is always massive, reaching up to the highest levels of power.”

In O’Reilly’s words, “There’s a very secret plan…to diminish Christian philosophy in the U.S.A”; in Gibson’s telling, “I began to connect the dots and discerned the outlines of the conspiracy.”

I think this is what is at the core of the "War on Christmas" crusaders.  It is not a counterattack against a perceived "attack on Christ" — it is, at its core, bigotry against non-Christians (whether they be atheist or members of other faiths).