The lack of a Facebook app for the iPhone hurts Apple more than it hurts Facebook, in my opinion. Facebook has a near-monopoly in feature-rich social networks (yes, the specifier was inserted to discount Twitter, but I believe Twitter has a very different market/userbase from Facebook and isn't in direct competition; I'd be happy to argue about it) and its most threatening competitor, Google+, probably isn't going to have a native app for iOS anytime soon.

In addition, a native app will make it actually harder for users to run Facebook apps; apps that require micropayments will be especially problematic within Apple's framework.

Is the user goodwill from releasing an iPad app worth potentially driving users away from Facebook apps? Probably not. Apple, on the other hand, lives and dies by user experience.