Everything isn't running on the Internet. When you use Google Voice to call a number that isn't part of GV (which is probably the majority of calls), your call is going over the PSTN. And touching the PSTN is what gets you regulated.
Facetime is a good example of a system that isn't and shouldn't be regulated because AFAIK it doesn't touch the PSTN.
But touching the PSTN isn't where VOIP gets regulated under the FCC rules. If you have Vonage and only make VOIP to VOIP calls, you still pay the tax.
That's the whole point of bringing up USF: one can imagine ways to limit the USF fees to the PSTN network, but the FCC has used its regulatory authority to reach a broader set of service providers. Also: the PSTN angle is a red herring anyway. Now that USF is used to fund broadband, its arbitrary to limit USF taxes to something that touches the PSTN network.
Facetime is a good example of a system that isn't and shouldn't be regulated because AFAIK it doesn't touch the PSTN.