Of course this would happen. There's all kinds of competition from two sides, other mobile-pay companies (and systems) on the one hand, and the established credit-card companies on the other. And this kind of competition involves all kinds of pressure, subtle as well as blunt, to "encourage" retailers to do it their way. It's a no-holds-barred free-for-all right now, and, while there might never be a clear winner, some will lose out, and go the way of the Edsel. I hope it's not Apple, but it could be.
An uncomfortable truth for Apple: is it really all that hard to swipe a credit card, an established, globally well-known system which we already have, incrementally updated to increase security - and thus, would entail no additional system revamp or hardware investment for most retailers in the world? What, for the average consumer, makes ApplePay more attractive than that - beyond the "cool" factor?
The credit card companies actually support Apple Pay. They've been putting some serious marketing dollars behind pushing it too. It's more convenient, infinitely more secure, and will encourage consumers to use cards more than they currently do. They make a lot more money on interest rates than they'll lose from the fraction of their fee that they'll pay Apple.
Additionally, the US magnetic strip credit card system is archaic when compared to the rest of the world. Most countries have switched to contactless cards already, which are far more secure than what we use in the US. It's a long standing problem that has put US consumers' card data at risk time and time again.
In 2015 the card processing rules are changing. All cards will support a chip system and retailers will have to upgrade their processing machines to accept them. If they don't, they'll be liable for fraudulent charges resulting from data theft, stolen cards etc.--not the banks (as is currently the case).
Retailers must make upgrades anyway, NFC capability isn't necessarily an expensive add-on and most companies are pushing those machines hard.