There's merchants of record like Paddle.com that do the exact same thing (handle taxes on software sales for you) and they charge 5%. And that includes payment processing fees they have to pay to Paypal etc.
So with Apple's scale, they could easily offer this service at below 5% commission.
You're paying for access to iPhone users, not the transaction fee.
An analogy would be, creating a product and getting on store shelves. You pay the store owner a percentage of each sale, in order to be sold in the store
