The Apple iPhone is such a popular device that it has encouraged a huge number of 3rd party developers to write applications for the iPhone, and Apple makes a large number of them available on the iTunes store (Apple claims that around 20% of the 500 apps that it receives per week are not approved - either directly rejected, or they need some modifications). However, it is apparent that one area where Apple is most concerned about is apps that either affect Apple's or AT&T's data plans or the money they make from voice calls. There was a lot of controversy in the month of July when Apple rejected the Google Voice (learn more) application, a software that could enable people to save money in making calls (even if Google Voice is not a VOIP application). The FCC was concerned about this apparent rejection, since it would seem that customers were being denied an alternative, and asked Apple for an explanation.
Apple has finally replied to the FCC, giving multiple reasons for the rejection, including privacy issues, and an apparent change of the basic call making flow inside the app (link to article):
"The application has not been approved because, as submitted for review, it appears to alter the iPhone's distinctive user experience by replacing the iPhone's core mobile telephone functionality and Apple user interface with its own user interface for telephone calls, text messaging and voicemail," Apple said in a statement posted on its Web site. Apple also said Google Voice's importation of the Contacts database represented a privacy concern. "[T]he iPhone user's entire Contacts database is transferred to Google's servers, and we have yet to obtain any assurances from Google that this data will only be used in appropriate ways," Apple said.
Separately, Apple acknowledged that its agreement with AT&T obligates it "not to include functionality in any Apple phone that enables a customer to use AT&T's cellular network service to originate or terminate a VoIP session without obtaining AT&T's permission.
However, Apple is stating that the application is still under review, and not rejected; an apparent subterfuge to ensure more time, and maybe hope that back-channel contacts ensure that the issue goes away.
At some time in the future however, Apple will find that the platform that it has built in the form of the iPhone and the app store will be broken open, that Apple will find that the rights it has to deny an application will need more openness. This could happen through a mix of consumer reaction and pressure from regulators.