According to Noyes, while banks control the card-present/not-present rates, the networks negotiate the rates with payments processors. The differences can be dramatic. Apple was apparently adamant about getting the card-present rates and told issuers that it would assume some of the fraud risk inherent in every transaction by providing a secure element via biometric authentication (its TouchID feature) and location data provided through an NFC chip. The Apple payments platform will work with all of their cards.
Banks offered the discounted fee for two reasons: for the Apple payments platform to accept all of the cards from the issuers, and for Apple to assume some of the liability by including two secure elements that will authenticate transactions — location data via the NFC chip, and biometric security. This is essentially a wash for the financial services industry: they lowered fees for Apple for the privilege of being included in Apple’s payments initiative, but managed to put some of the transaction risk to Apple.
If all of this is true, it’s potentially massive. And it may speak to why Apple may have finally greenlit the use of NFC technology in their products, even though they could have presumably done everything they wanted with the already-implemented Bluetooth LE tech.