Submission + - Apple Said to Negotiate Deep Payments Discounts from Big Banks (bankinnovation.net)
Basically, there are two kinds of credit card transactions: card-present, and card-not-present. The former is cheaper because there's less risk of fraud. The article says that Apple has negotiated the card-present rate for its iPhone payment system, even though the card is not present. Presumably, this is because of some other security features that reduce the risk of fraud.