The network is not able to handle the load now and if they allowed Skype, Sling and others it probably be even worse. Though if iPhone was not exclusive to them, a lot of their problems would be solved!
Although just recently released GV if released on the iPhone would become a staple app; free SMS. Thus, with everyone using it would put a further strain on AT&T's already drained network, as well cut into PROFITS. So, it could possibly be both.
http://www.techcrunch.com/2009/07/29/att-dont-blame-us-for-t...
Also these applications exist and are allowed on other phones on AT&T. Of course the popularity of the iPhone, bundled with the App Store single point of distribution makes it possible for AT&T to insert themselves and have any control. Perhaps if they'd be willing to build out their network more instead of fighting the future.