That is because the person who does the billing incurs the costs...the billing isn't based on usage, it is based on who processes the bill.
They could have a standing charge for each app, with charges per thousand downloads, for instance, which would more closely follow their actual costs, and charge 5% for payments. That would have a different set of positives and negatives, but the way they've chosen is just one way amongst many options they've got.
When apple gets control over the transaction, they can take whatever cut they want