As an ethnically-Indian Canadian-born resident of Australia, my go-to answer to "Where are you from?" is "Canada".

I have no problems with the question itself, but oftentimes it becomes clear that the person asking it isn't satisfied with my answer. They want to know why I have brown skin. In these situations, "where are you from" is just a euphemism for "what's your ethnicity". I don't think either question is offensive in the slightest. But it's definitely annoying when people ask the former when they are really asking for the latter.