This depends on various things:
1.) If anonymous mit chips operate like a wallet then there will be no charges besides purchasing the chip card. This is the major use in Europe (bus-tickets, ATM Payments,Internet payments etc.
Banks could charge transaction fees for charging the card only, because the rest is anonymous and hard to track. e.g.: I donate something now and transfer money to the E-Wallet of my buddy later. etc.
This is the typical use case here in Europe.
2.) In case transactions are not anonymous, timestamped and signed transactions could be transferred to the authoritative issuer on every recharge or payment and then be charged.
This is not used here in Europe since the system shall work like a wallet.
Transactions are anonymous. The value message that is used to transmit the actual money is cryptographically tied to a particular recipient. There is no way to collect fees from the actual transaction itself. No fees are inherent in the system.
App developers, however, can choose to charge for their apps and the service of using them. It's up to developers' discretions.