Backup.
Banks take a certain percentage of transactional charges based on the particular retailer and what that particular bank agrees on (one of the reasons Square has done well, they have the lowest fees for merchants compared to JPMorgan Chase Bank, NA, Citibank, Citizens, etc). Apple Pay does not take a higher percentage [if at all] and no statement suggesting such has been claimed by the banks or Apple. The banks are covering the costs as it 1) saves them money from less fraudulent transactions with increased security via NFC, TouchID and tokenization 2) as no personal data is passed, only a one-time transaction token, credit cards do not need to be re-issued should another Target or Home Depot security breach occur.
As Apple Pay's securer [at this time] payment system will save banks money, the banks are covering the costs. Apple nor the banks have suggested there is a large [if at all] take on Apple's part. If there is, even that percentage is still less than what banks would lose in the current system.
Again, this is not an Apple Pay matter, this is a matter of MCX strong arming merchants into exclusivity through kickbacks as MCX sells consumer information to marketers. This is about stifling technological advancements with NFC systems. If you're seriously suggesting Apple is trying to monopolize the system, wrong. Apple Pay does not stop other forms of payment, it is another form in addition to what is currently available. According to security experts and banks, it is currently the most secure payment system available. The only reason MCX merchants are suppressing it is the strong arming of MCX pay merchants for participation (either play by their rules or lose your kickback).