Walmart, CVS, Target and others are moving towards adopting the CurrentC mobile payment system so they don't pay 2-3% on every transaction made by credit card. It makes no business sense for them to support Apple Pay.
Will CurrentC take off? I don't know. It's kind of clunky.
It makes sense if they are going to lose a lot of business by not supporting the payment. Why do you think a lot more businesses accept Amex despite the fact that amex charges more than the other cards and also is more likely to take the customer's side in a dispute (This is why Amex isn't as accepted as other cards but I've noticed over the years more and more stores are taking it including small, local stores). Because Amex has gotten so popular now they are losing out on business by not accepting it (and there are people who won't shop there if they don't take Amex).
It's also why you see more and more stores take credit cards, even small stores. It's very rare these days to find a cash only business (I know of one restaurant, a Pho place with cheap bowls of Pho). Because they lose too much business by not accepting them.
Otherwise, your argument would argue that you shouldn't see stores taking credit cards cause all the problems you mention about NFC pretty much are more the problems with accepting credit cards.
Now, they'll try to push people into using CurrentC in hopes that maybe at worst they'll pay less fees as maybe fewer less will use CCs. And at best be popular enough that they can start refusing CCs entirely (I doubt that will happen though unless they offer really good perks for CurrentC. And they're going to have some hurdles with CurrentC being way too much of a hassle to use to really take off and add the more security minded aren't going to like them wanting access to their bank accounts and worse, their SSN. Anyone smart will balk and not sign up for the SSN requirement alone. Crooks can do a lot worse with your SSN then they can with your CC number or even your bank number).