Wasn't that because Apple wants 30% off all sales? Microsoft had a similar clash with Apple over Office for iOS. The apps were free, but if you wanted to buy a license to use them, you would have to purchase that license directly from Microsoft because Apple wanted a slice of the upsell. This would have added a 30% tax on top of the universal service fee Microsoft was selling, even if it was just a link to the website from within the apps. I don't know how that was finally resolved, but this is just how Apple conducts business.
