The problem here are not the special deals, saurik commented he cut special deals in the Cydia store occasionally the last time this topic came up. The problem is that there is no alternative to Apple when it comes to publishing software and content on the iPhone and that makes these kind of deals unfair.
Even if the app store was run differently, say allowing a competing way of installing apps, Apple still have plenty of fungible power to make such deals. You might have ticked a box to make it technically fair, for some definition of, but that would probably be just cosmetic. IE, app store would still represent most revenue and everyone is in the same position but a few geeks.
The "platform game" establishes market power, where buyers and sellers need to go through you. They have no negotiating power, and you can price to make deals that take all the "surplus utility" off the table, in classic economic terms.
So... reality isn't perfect and some players are big enough to negotiate. Netflix is that player here. They negotiate when they have to, but try to keep it quite.
When the market is this structured, this is how it works.