Well... as far as someone actually saying to you, "Happy holidays" instead of, "Merry Christmas," I would at least give them the benefit of the doubt on that one man... I mean, how does that person know what holiday you celebrate? It probably cuts down on a lot of awkward little moments where we have exchanges like this:
"Merry Christmas!"
"Um, I celebrate Hanukkah, I'm Jewish."
"Oh, sorry."
So, yeah, as far as that's concerned, I think that's just cutting down on going through those little to-dos.
But yes, you're right, in some cases, the word "Christmas" (and yes, nativity scenes) can be offensive, and in this day and age, it's safe to keep one particular group of people happy as opposed to others. Apparently, it's better to remove religious references to avoid offending irreligious people than it is to keep religious references in to avoid offending religious people.