Sure Apple makes money off their share of the payment system. Why shouldn't they? They built the whole thing from scratch, including the phones it runs on.

Also Apple doesn't just support the secure payment system, they also handle distributing the money and providing customer support to the end user and the developer. That isn't free either.

If you don't like the Apple model, there are alternatives.

Apple's argument (which seems compelling if we judge it on the result) is that their model is the best solution for customers and developers.