Apple Pay does not cut into WalMarts margins at all.
Retailers pay a fee to process credit cards transactions through a clearing house which is operated by Visa/MC 1-3%, sometimes a flat minimum fee, it's all negotiable based on quantity of transactions. More transactions = lower fees.
Accepting ApplePay does not cost a retailer anything, except the initial startup cost related to nfc terminals. ApplePay is seen like just another credit card transaction.
Apple cuts into the clearing house costs, the already agreed upon 1-3% fee. A fraction of that is paid to Apple by the clearing houses.
NOW, companies like WalMart are greedy. They want to avoid the 1-3% fee alltogether. They are basically building they're own clearing house/wallet/all in one solution. It's messy and requires scanning a qr code, then presenting to the cashier, a lot more complicated than swiping a card never mind Apple pay, but saves a lot of money on payment processing fees.
The companies figure if they all band together, their billions and billions of dollars of sales will let them bargain to reduce the transaction fees on remaining credit swipes, and increase profits due to lower fees.