As a Minority New Yorker, I will have to say that I don't think it's the south in General.
When I was traveling in my own state, the smaller the towns became, the more I got looked at. The same type of people the OP spoke of lives about a hour north of me. Not that many people realize that. Country music (the galvanizing sound of Hillbillies and Rednecks the world wide according to 'experts') and rock and roll are the only things on the stations 30 miles north of me, and I live in a suburb of New York City (as the rich people claim it to be).
I think what really happens is the same for all peoples in the world. People congregate with 'their people' The most 'racially diverse' city in the world proves that. There's a reason there are Chinatowns and Little Italies and Spanish Harlems. Given choice, people want to be with similar customs for the feeling of support and kinship. From there, pride is born and... as we all know, Pride becomes before the fall.
Ignorance or outright blasting others that they don't have any way of knowing about or choosing the path of outright ignorance because just as hereditary as facial features. If you're a child, and you hear 'those people aren't like us', you start to wonder what's wrong with them. Obviously, we are good, and something is off if you're not us. That's easier to breed in small towns. Because like it or not, in New York City you will have to travel where the other races, cultures, and creeds are. You can't live in one section of it. But smalltown usa? Mostly self-sufficient and have no need for anything that's not in a 3 mile radius? Those beliefs can easily become reality.
Now, why did I say this? People consider the south to be rural, aka those smalltowns that don't have a need for anything beyond that arbitrary radius. Hell, we even know racists live in New York city. We deal with them all the time. But we have a support system here that if we DO find the idiot who says it, we can get the cops on him.
Smalltown Usa? Where everyone for a ten, twenty, or thirty minute drive expressly is not like me and probably has the same ideas as this guy who just insulted me? Yeah, I'd feel pretty much screwed and will just want to get into my car and book it.