It’s because the question gets weaponized or used as a micro-aggression. Because of a person’s skin color they can’t possibly be a “real” American, right? Usually, the person can tell by your tone of voice or phrasing when you ask the question whether you are just curious to learn more about them or if you’re a racist dick. But either way, the question comes at them so often that they bristle when they hear it even when it is asked out of curiosity.