Why would CVS or RiteAid want Apple Pay anyway? If a shopper has bothered to come to the store, select items to buy and then go checkout, chances are they want the items relatively more than someone who hasn't gone to that effort. The stores of course support several different existing methods of payment which work just fine from their perspective. The customer is likely to pay anyway.
Perfect? No. There are middlemen involved in the transaction but it's a system everyone more or less tolerates. Extremely complicated financial deals are behind every card terminal you see in a store. None of that stuff just happens. It's all very carefully planned.
Along comes Apple which puts themselves into play as yet another layer of middlemen, one which the stores have zero control over and one which is outside their established payment process. It also runs counter to their own payment initiative which they have agreed to support exclusively. So what Apple tried to do was an end-run around the established players AND they did it using the existing installed card terminals. NOBODY piggybacks like Apple tried to do without having some major skin in the game. You try stunts like that, you are going to get your hand burned.
So, Apple is at once both another layer of middlemen interference and also potentially a contract issue for the other payment product. Apple was too late to the game. And from the store's perspective again, you have a cart full of stuff, you aren't going to just walk away, you'll probably pay with another method so they have nothing to lose really buy rejecting Apple Pay. Same for GooglePay which I never saw in the wild. Whatever.
Apple has a habit of intruding on entrenched turf and taking on the existing players. They did it with phones. But payment systems are a much more spread out target where everyone has their own idea of what they want and most of them think it works just fine as is, including the customers. Nobody who mattered much was asking for NFC payments. Apple has been pushing this, suddenly, so it's up to Apple to tell everyone why they should want it. It's totally on them. Until they do that, until they make some inroads at the card terminal issuers, Apple Pay is going to be limited.