We have seen at least one company that lets you place Skype calls from your iPhone. But so far, this has been been through a call-back. This is not end-to-end VoIP. You are still using your airtime. Because of this, I am sure AT&T doesn't mind too much.
What I hope to see in the near future is a true Skype client running on the iPhone. I don't expect it to work well over GPRS, but you will be able to use it over Wi-Fi.
Because the iPhone is a closed platform, creating a Skype client for the iPhone will require a number of hacks. This means that most likely we won't get an "official Skype client" for the iPhone. And because the Skype system itself is closed, we haven't seen a lot of third-party Skype client for any platform. Creating one for the iPhone will be a double-challenge!
But ultimately, this will be done. And at that time it will be interesting to see how Apple and AT&T react.