Apples and oranges.

Apple Pay has no fee to the user or the company receiving the money, it's paid by the bank and is EXTREMELY small. Normal credit card fees still apply, but those don't go to Apple. For all intents and purposes it is a single bank transaction almost like any other. Apple has almost no part in it except helping verify security.

In-app purchases are different. Apple takes a cut because Apple provides a real service. They host the app, they do the billing, they do the collections, they do the license tracking. They handle taxes in all sorts of countries in different states. They make sure their store complies with all local laws. They handle security and try to stop piracy. In short, they're providing a lot of services.