This is exactly it, and exactly why I'm going to stop shopping at both Rite Aid and CVS, despite being a regular customer of the latter and occasional customer of the former.
If they weren't equipped for NFC payments, I might be mildly annoyed once such a thing is more common, but there's a legitimate reason--new PoS terminals cost money to buy and install. If they've chosen to not accept any fee-added payments (like, say, Winco or some gas stations), then there is a legitimate reason and the savings are theoretically being passed on to me (definitely in the case of gas stations, since you can compare the price to the more expensive place across the street that accepts credit cards).
But if you already have the hardware to accept NFC payments, and already accept credit cards, and the only reason you won't accept my method of payment that uses both of those technologies is that the value-added-for-the-retailer payment processor you've chosen doesn't like competition it is exactly the same as if a store accepted only MasterCards issued by Chase. That's your prerogative, but if I have a BofA MasterCard, I'm certainly not going to go get a new card, or spend the time to go to an ATM and get cash, just so I can shop at your store.
Or, looked at a different way, if CVS and Rite Aid have decided that the security of my personal financial information and privacy, as a customer, are less valuable to them than whatever processing fee and tracking benefits they will get from MCX, then I will take my business elsewhere. They made a calculated business decision, and I am doing the same.
It's not knee-jerk, or Apple fanboyism, or reactionary, it's just a logical business decision on my part, just like they made. The only question is whether there are enough people like me for the financial hit they're going to take of losing customers to Walgreens to outweigh the benefits they may at some point realize down the road from reduced fees and better tracking info from MCX.
One of the great things about the entire credit card system was that it "just worked". Now we're getting into payment wars for absolutely no logical reason other than improved margin and ability to track customers.