I am genuinely confused over the strong negative reaction you have here. First time I have seen such a thing, and I dare say similar things would apply to most of those that quoted you on it. I could possibly understand if you were mischaracterised it might get tiring for some, and a further failure of geography ("I'm from the UK" "oh I once went to Sweden" sort of thing) can also not help matters, but the mere question asked because the person is curious is never something I would have considered any kind of poor form to ask. Equally I can't see the mere question belay any desire or notion that someone intends to treat someone other than as a person.
There are questions and lines of conversation that have implications; I think I joked before that if someone asks me about my job then it is as big a clue as any that I am speaking to an American, and similarly if someone is telling me about their kids then I only really care if I know said kids in and of themselves. Again though a simple "where are you from?" is plenty innocuous as these things go, and actually a useful question.
To further answer the question of "why would someone's country of origin matter?" then if I am seeking common ground (fairly common in conversations with new people or people you are attempting to get to know better) then one's country of origin tends to provide a starting point for all the various forms of media and entertainment, geography, history, food, language, industry, politics/current events, sports, science and if I must be British about it then even the weather. It gets even better if your general hobbies are a bit obscure to begin with; I can't say I meet many ROM hackers or people interested in the maths and manufacturing of old school heavy engineering*, some like old machines but the approach there is quite often radically different, and if I start talking about anything that with a completely random person it tends to go nowhere and makes me look very strange.
*choice video
*snip*