It's crazy to think that anything you do inside your app between you and your customer is subject to Apple forcefully inserting themselves into the relationship, and then demanding payment.
Apple's marketplace is inside the App Store, not inside the apps that are developed independent of them. You could argue that the apps are not developed independently, as they could (not by choice) use Apple's APIs, but I feel that that is what the $99/yr developer fee entitles the developer to use.
To the general problem; I really hope Apple stops being anti-consumer and anti-developer using these landlord tactics. The (second?) richest company in the world does not need to take these extra commissions. Without these developers, there would be no App Store, and it's in Apple's best interest for them to thrive. Apple is making the calculated decision of how much they can take off the top while still having developers make good products for their platform. Yes, their investors will not be happy that a source of income is being lost, but it's up to Apple to convince them that the good will from consumers and developers will provide more value through other means than that loss of income.