It is a lot more complicated, and isn't about * Pay type services
I don't think companies like Visa, the banks that issue cards, or the processors have a problem with Apple Pay, the percentage they collect is so tiny it hardly matters. The merchants are the ones with the issue, but not so much with Apple Pay but with all the rules and expenses the shift to EMV has imposed on them.
It might not seem that bad for a small shop with a single checkout, just replace the little credit card machine, right? The problem is that typically the POS vendors won't support that with existing hardware/software so they need to upgrade their POS hardware and software to support the EMV reader, saddling them with thousands in additional cost where of course the EMV promoters were talking about how inexpensive it would be since only the readers would need to be replaced.
Think about restaurants, in the US the standard way you checkout is to give your card to the server, who goes to a POS terminal, swipes it in a reader that's built into it, prints a receipt, and brings it back for your signature (yeah, I know you right ponders are rolling your eyes at this scenario) That won't work when EMV is fully implemented and uses a PIN instead of signature, because the card owner will need to type in the PIN themselves.
So restaurants will need portable readers they can hand to the customer to do their thing, and if the customer wants a printed receipt either a portable printer or walking back to a POS terminal to print it. Then they need to add a secure wireless network (they can use WPA2 to insure it is secure....oh wait...) for the portable reader to talk to the POS system for the amount, and to the processor to handle the card. And of course they'll need update to all their POS hardware and software, including the back office 'server' that manages all the terminals, just because, because the POS vendor isn't going to pass up an opportunity to soak them.
The thing is, currently the only pressure being applied to retailers so far is a liability shift. Previously if someone used a stolen card or otherwise disputed a card, the bank took the hit. Now if a retailer processes a non EMV transaction with an EMV capable card (except for a few exceptions that are given longer to be compliant, like gas pumps) and its disputed, the retailer takes the hit, not the bank. So businesses that rarely see disputed charges have little pressure to upgrade, they can take their time and wait for the technology to mature. Businesses that see a lot of chargebacks haven't had the luxury of waiting, and unfortunately businesses in more crime/fraud prone areas were probably least able to afford it. It will be a few years (I don't think there's even a date yet) before the change is forced, by banks refusing to process non-EMV transactions at all.
This is why you see recently opened places that bought everything new, and some major chains (especially those which already had aging POS systems so they would have had to replace them anyway) able to support Apple Pay, but most of the smaller locally owned type places are still doing the swipe thing.