I actually have been asked what country I am from. I don't have a heavy accent (there are far heavier than mine further out in the boonies) but apparently enough of one.

What of it? If you have some characteristic that is unusual (within a group such as local community) people will notice and be curious.

That is basic human nature, not lack of friendliness or malice.

It's prodding into personal details that many draw the line with. You might not have a problem with it, but I've personally heard from a few different people how they get annoyed with those sorts of questions being leveled at them all the time, simply because they didn't look white. Aziz Ansari even joked about this a few times during Parks and Recreation, it's such a common phenomenon. Imagine seeing someone who might have some sort of disability then asking them if they were insert disability you are unqualified to diagnose but assume they have. That would be considered pretty rude.

This might just be an issue of regional vocabulary though I'm sure it's used in the presumptuous way you describe as well, the underlying question isn't necessarily unfriendly or borne of a discriminatory attitude - in a Midwestern town right now, but I can recall a few weeks ago actually this exact conversation between my American friend who's from a Pakistani background and a female census taker who was from South Asia.

In her case, she used the exact same vocabulary but it was much more obvious she didn't mean to imply that they weren't native born because she herself was not native. Context is important in conversation, but there is such a thing as regional mannerisms. On the west coast my vocabulary was certainly brought up for being just a tinge different.