It appears that Rite Aid and CVS are completely disabling NFC in their payment terminals in order to block Apple Pay. John Gruber of Daring Fireball has a good overview of the story, as well as some thoughts on what's likely behind the action (well worth reading). John confirms what I suspected:
And the reason they don’t want to allow Apple Pay is because Apple Pay doesn’t give them any personal information about the customer.
Loosely Related: How Companies Learn Your Secrets - The fascinating story of what happened when a statistician for Target was asked, “If we wanted to figure out if a customer is pregnant, even if she didn’t want us to know, can you do that?”