Nobody's trying to take Christ out of Christmas. Kinda hard to call it Christmas without him.
Secondly, Christmas is NOT the only holiday being celebrated this time of year. We have Hanukkah, Kwanzaa, Yule, etc. Stores have to be respectful of their multicultural customers, therefore, saying "Merry Christmas" to everyone is quite presumptuous and, well, rude. Not rude to Christians, of course, but to anyone who isn't, it's rude and insulting to presume they worship a religion and thusly celebrate a holiday that they don't.
After all, as a Christian, you wouldn't want to be wished a Happy Hanukkah, would you? You're not Jewish, after all. Saying things like "Happy Holidays" or "Seasons Greetings" can allow stores and their clerks and any other business to wish you a happy holiday season without insulting you by trying to assume what religion you are and wish you a Happy Hanukkah when they should be saying Merry Christmas.
In my opinion, this whole "war on Christmas" is a load of baloney cooked up by the media and likely the extreme end of the conservative religious spectrum to get attention and force their beliefs on others. Whether or not to say "Happy Holidays" or "Merry Christmas" is hardly something to start fights over. It's words. Be glad that you're wished anything at all besides the usual "have a nice day".
And for the record, I'm an atheist, and I don't get myself in an uproar anytime some clerk around here wishes me "Merry Christmas" or "Happy Holidays". Christmas isn't the only holiday celebrated this time of year in this country, so get used to the "Happy Holidays" and get over it.