Apple Pay charges much higher rates than competing payment processors.
Apple Pay isn't a payment processor. It's a system for banks to provisional additional cards on their customer's devices, which are then processed the same way and for the same fees as tapping the physical card.
Banks want direct access to the NFC because they want to bully people into making their app the default handler for payment cards. One of the great things about Apple Pay is that all banks must compete as equals for every transaction. It's trivially easy to switch which card you use when you pay and every card gets the same best user experience.
Forcing NFC open is, paradoxically, anti-competitive, because it makes it easier for the biggest banks to stop competing and instead lock their customers in.
Merchants do not have any relationship with Apple for Apple Pay transactions. You tap your phone and it's treated the exact same way as when you tap your card. The merchant sends it to whoever they use for card processing, who eventually sends it to the card network (Visa, etc.) and to the bank for approval. That's what payment processing is. Apple isn't involved at any step. They are involved in the provisioning process where cards are added to your device.
Apple charges a fee to the issuing bank, which comes out of their share of the card processing fee paid by merchants. The original (2014) reported fee for US credit card transactions was 0.15%. Card processing fees are, in general, significantly cheaper in Europe (and indeed most other countries). We don't even know if the US fee is still 0.15% but it definitely isn't in the EU.