Yes.
Credit cards are a bit of a different beast, but I presume most of us have annual fees, plus interest on monthly balance. VISA and stores handle most liability risk. I believe in case of contactless payment vendors like Moneris there are a combination of fees paid by the store. Apple will be taking a % of that revenue.
Bank debit cards... My wife works at a bank, we keep a high minimum bank balance, and therefore no monthly fees, and unlimited NFC transactions. Most I'm sure if they have a minimum balance have some sort of base fee paid each month. Banks handle disputes directly with users. If ultimately a store is paying same price for a POS NFC terminal, and use fees remain the same, there's a likely sizeable bit of revenue Apple is profiting.
If I was watching every penny I was paying, I would presume it is healthy enough of a cut worth fighting in court to help limit costs. Instead of using our manufactured/secured NFC cards, we are wanting to use your hardware instead... let me pay you Apple, a standard fee for use of that NFC chip not based on transaction amount. Or, argue to a judge nothing. There are third party apps freely using the NFC chip to read/write data already.