According to The Daily Dot who spoke to several different banks who are working with Apple on the service, it sounds like they are quite confident in the security of Apple Pay, so much so that they will be assuming all liability for any fraudulent purchases that might occur. According to USAA assistant vice president Vikram Parekh, “The bank has liability for any purchases made when Apple Pay is offered and used as the form of payment. This is true for both face-to-face and for “in-app” purchases.”
Other banks such as Chase and PNC have offered up similar statements, thus indicating that they too believe that Apple Pay will be secure. One of the ways Apple is securing Apple Pay is through the use of Touch ID, where the purchaser has to authenticate the purchase using their fingerprints on the Touch ID sensor found in the iPhone 5s, iPhone 6, and the iPhone 6 Plus.
It will also work with the Apple Watch where the sensors underneath the watch will authenticate the user, and if the rumors about Apple’s next-gen tablets are to be believed, they will feature Touch ID sensors that will support Apple Pay as well.