That is pretty messed up. There can be gazillion good reasons for somebody to stick out, or somebody else to just asking. People getting easily offended and taking such benign question very personally have usually some deeper underlying untackled issues in their lives.
It never even occurred to me people might be offended by that. I love stories of different places and foods, and I'm fascinated by all the permutations of accents that occur. I'm simultaneously mildly angered by people being offended by such a thing, and that others trained them to be that way.
I get asked where I'm from all the time even though I'm very obviously from around. I get what you mean but differentiating curiosity from xenophonia is generally pretty easy, and as such I see no reason why we should avoid the question entirely. Intention and context counts, pretending that it is always an offense is absolutist and reductionist.
