In Chicago you can put your metro card in your apple wallet and it’ll automatically use it on the public transit system even if you have a different default set. Not sure if apple is charging them fees or what, but it works pretty well for me.
IIRC, those fees are charged to the merchant in order to process transactions. Traditional credit cards are similar in theory. For example, American Express has long had the reputation that in addition to the cards people know (Green, Gold, Platinum, etc.) technically being "charge cards" that need to be paid in full each cycle, merchants pay a higher fee to accept them.
^ Offset of course by the fact that most customers have pretty good credit to begin with and probably spend more than your average Visa or Mastercard.
In addition, I would also expect them to be paying for integration into someone's payment infrastructure to provide other services - PayPal, Stripe, Square, and the like.
