Many smaller banks and credit unions already operate at super slim margins, and cannot afford the per purchase payment that Apple demands in return for letting banks register their customers.
It's just another example of a greedy large entity slowly destroying small town life. Small banks and credit unions expressed worry about this when Apple Pay came out. They're trapped, with a join them or lose some customers dilemna.
As to what you could do, hmm. I'd say to volunteer to pay the Apple fee for them, but Apple's rules forbid passing on the cost to the consumer. Or.. you could talk all your neighbors into letting the bank raise its rates.