I objected strongly in my HS to the practice of foreign language classes learning a carol in that language and then singing it in an all-school assembly. The idea of learning a song in language class seems great; it provides a practical experience. But making it a carol made (and makes, to this day) non-Christian students uncomfortable. (BTW, my "reward" for writing an opinion piece in the school paper on this topic was someone etching a swastika into my locker.) Obviously, that's horrible if someone etched a swastika and I hope the person was caught/punished. I got similar treatment because I didn't believe in anything. (Though my personality was perverse enough that I rather enjoyed the reactions)
But I still have a question about the concept of being made to feel uncomfortable/unwelcome. Those are nearly impossible to evaluate, and there's a real slippery-slope. There are already people in this country who feel making kids recite the Pledge of Allegiance (not just the "under god", but the entire thing) can alienate them. I don't claim to have all the answers on this - I don't think anyone can - but I personally have never been impressed with the merits of the "uncomfortable/unwelcome" argument.