I needed a couple of grocery items and happened to be next to an Amazon Fresh. Cool, let’s try it! Went in, found everything I needed and went to self checkout. When it was time to pay, the machine wouldn’t accept Apple Pay. I ask an employee who helpfully informs me that I can pay with physical cards or my Amazon account.
I didn’t have my physical cards, nor wanted to do my Amazon account so I had to leave empty handed. Why don’t they accept Apple Pay? Because they can’t track you. If you use a physical card, they can likely link that card number to an Amazon account and thus attribute the purchase to a person. If you pay with contactless payment they get a one time token that they can’t tie to anyone.