In a letter to the FCC, AT&T acknowledged that Apple and AT&T have an agreement to block VoIP apps from using AT&T's cellular networks, but that VoIP apps that use Wi-Fi are OK. Here's a selection from the letter.
...AT&T and Apple agreed that Apple would not take affirmative steps to enable an iPhone to use AT&T’s wireless service (including 2G, 3G and Wi-Fi) to make VoIP calls without first obtaining AT&T’s consent. AT&T and Apple also agreed, however, that if a third party enables an iPhone to make VoIP calls using AT&T’s wireless service, Apple would have no obligation to take action against that third party.
The parties’ concurrence on this provision was particularly important in light of the risks the parties assumed in bringing the iPhone to market.
...The parties’ willingness and ability to assume the risk of their investments in the iPhone and of their pricing strategy were predicated, in significant part, on certain assumptions about the monthly service revenues that would be generated by iPhone users. In particular, both parties required assurances that the revenues from the AT&T voice plans available to iPhone customers would not be reduced by enabling VoIP calling functionality on the iPhone. Thus, AT&T and Apple agreed that Apple would not take affirmative steps to enable an iPhone to use AT&T’s wireless service to make VoIP calls.
Without this arrangement, the prices consumers pay for the iPhone – particularly the broadband-enabled iPhone 3G – would likely have been higher than they are today. ... During the course of the agreement, AT&T indicated to Apple that it does not object to Apple enabling VoIP applications for the iPhone that use Wi-Fi connectivity ... rather than AT&T’s 2G or 3G wireless data services. Although AT&T has no involvement in producing Apple’s iPhone Software Development Kit (SDK), which establishes the iPhone functionalities accessible to application developers, AT&T understands that the SDK enables application providers to develop VoIP applications that use the iPhone’s Wi-Fi capabilities and that such applications are currently available in the Apple App Store.
As noted above, AT&T regularly reviews its policies regarding features and capabilities available through the devices we offer in order to provide an attractive range of options for our customers. Consistent with this approach, we plan to take a fresh look at possibly authorizing VoIP capabilities on the iPhone for use on AT&T’s 3G network. AT&T will promptly update the Commission regarding any such change in its policies.