Apple worked it out with Visa/Mastercard they they get a cut of the interchange fees, so the retailer pays no extra fees from what they would normally pay.
The retailer would only pay the Stripe fee. If I understand correctly, Apple collects some fees from the bank (that they take from the interchange fee)
Cristina from Stripe here. The merchant/retailer only pays the Stripe fee (https://stripe.com/pricing) for Apple Pay transactions.
From the perspective of the retailer, the merchant is charged the standard Stripe fee (2.9% + $0.30).