2. As part of that entitlement, you agree to pay Apple a 27% commission on any purchases made when users click those links, for up to 7 days after the link is clicked.
3. You agree to send Apple monthly sales reports.
4. You agreed to give Apple a right to audit your books at anytime.
That's the meat of it. It's a self-reported cost-per-conversion, which isn't exactly unheard of. Developers are in arms because they don't believe Apple deserves any money for distributing their app on their App Store.
That's the heart of the disagreement.
Apple believes they have a right to charge developers a fee for access to the users who shop through the App Store.
There are developers who believe that the App Store should exist as a free-thing Apple provides to developers, to encourage them to write software for the iPhone. They're willing to accept a nominal processing fee, but anything more is "anti-competitive".