The article you're linking to is not definitive. The source is anonymous and not confirmed:
"Under deals reached with banks individually, Cupertino, California-based Apple will collect a fee for each transaction, said one of the people, who requested anonymity because terms aren’t public."
This assumes banks make less money on transaction fees than they do on the other two when coupled with the potential for fraud... An interesting assumption...
Is this how it works? My assumption was that Mastercard, Visa, American Express, and Discover were the ones that made the % of each transaction and then the issuing banks were the ones that made the money from fees and interest.
Most of the fees end up back with the card-issuing banks. That's how they pay for the rewards programs, and why the fees are higher for rewards cards than other types.
It's my understanding banks also charge a transaction fee (may be flat per-transaction rather than a percentage.) (Source: I work for an online ticketing company, so we deal with these types of things.)