It really hurts the user experience sometimes. Kindle books are an example I hit a lot. Amazon can't do purchases in the app without using Apple's in-app purchase system, which would likely cause Amazon to sell at a loss. They also can't even link to their web site, which of course still allows payments even on the phone. So if I want to buy a book, I have to manually go out of the Kindle app, into Safari, go to Amazon, find the book I'm interested in, purchase it, then go back to the Kindle app and hope it synced. If Apple would be less idiotic here, I could be done with one touch.

And of course Apple has iBooks and doesn't have to worry about losing money on each sale because of a 30% transaction fee.