John Gruber is half right when he says..
And the reason they don’t want to allow Apple Pay is because Apple Pay doesn’t give them any personal information about the customer. It’s not about security — Apple Pay is far more secure than any credit/debit card system in the U.S. It’s not about money — Apple’s tiny slice of the transaction comes from the banks, not the merchants. It’s about data.
Data is part of it - It's not unreasonable for retailers to act to avoid others trying to muscle in on their customers and create a point of disintermediation but it's more than that. It also about fees.
Credit card interchange fees are substantial and if retailers can remove them from the value chain it will prove much better value for customers.
Unfortunately it looks like Apple Pay helps embed credit card fees and the 2 to 3 % they add to the cost of stuff, rather than help eradicate them.