As usual with languages, the anser is "it depends". The simple form ("where do you come from") asks the adressed person about their origin. If you were to ask me this, I'd answer with the country of my birth and upbringing. However, the progressive form ("where are you coming from") specifically asks where someone is coming from in an exact moment. If you were to ask me this I'd answer something along the lines "Right now I'm coming from work" or "from shopping" or something like that. P.S.: I'm not a certified linguist, just a language enthusiast with some basic observation skills. So there's probably someone that can explain it way better.