UPDATE: Both Apple and Sony have made statements regarding Apple's policy on in-app purchases. Sony feels that Apple's made the change with very little notice given to Sony, however, Apple says that they have not changed their developer rules or guidelines. They just require that if an app offers customers the ability to purchase e-books outside the app, the app should also offer it within itself. This policy should not affect the way Amazon or even Barnes and Noble function.
Apple is tightening their rein on the App Store by disallowing certain types of in-app purchases. Sony's application for iOS devices includes an ebook purchasing option (Sony's e-Reader Store) which clearly directly competes with Apple's iBooks. Apple's told Sony that all in-app purchases have to be cleared by Apple before Sony puts them up in their app. This move also affects Amazon, as their Kindle has promised Apple customers that they can have Kindle e-books without owning a Kindle. That may now change.
This could stem from the fact that Apple has made more money from selling hardware than music, apps and software. The move is also surprising because Apple has recently said that they want to be more collaborative with publications especially for the iPad. However, this is clearly restricted to magazine publications and not books per se.