Yeh a lot of stores, especially grocery, have loyalty cards that take care of purchase tracking.
There is also replacing all of those terminals (and especially those that were just updated to take chip) and back end software, training employees, and then labor to change it all over.
The Apple Pay fees are nominal in realty, I believe I read "0.15% of the 2% fee paid by merchants for each credit-card payment and half a penny for each debit card payment." So what, 15 cents per $100? They are offset by the better security and less fraud.
a LOT of it is internal company politics and alliances, not money