The difference between the potential of iTunes being used to access copyrighted material without payment and an eBook reader doing the same thing is that Apple do not sell eBooks.
Apple is ensuring that the apps on the iPhone make them money without any potential to cost them money. It's all upside for them.
Or, it could just be that the Apple Tablet thing, if it exists (10% probability) will read e-books (100% dependent probability), and therefore introduce a Book Store to complement the App and Music Stores (80% dependent probability, I'd say), and the iPhone and iPod Touch will inherit it (100% d.p.), and they'll want to shut out third-party Book Stores the same way they'd shut out a third-party music store (97% d.p.) and are willing to lie on rejection notices so as not to reveal their plan (20% d.p.).
Apple is ensuring that the apps on the iPhone make them money without any potential to cost them money. It's all upside for them.