Any company that contracts out their POS terminals and accepts credit and debit cards (so, just about everyone) can get a terminal that accepts NFC payments.
My local large grocery story (Albertson's, in southern California) has accepted Apple Pay from the start, even though their terminals don't look any different than anyone else's, and don't have the typical separate plastic thing that you're supposed to touch your phone to. The whole thing is built into the user-accessible terminal, and Apple Pay just works.
Stores don't own these terminals, and the companies that provide/service them can either turn on the functionality (if the terminal has it built in) or replace the terminal with a newer model (which happens regularly anyway). It's not a matter of having to run new lines out to the boonies - if they take credit cards, they can likely accept NFC payments.