I certainly don't know what the USB port is for, but I have an idea of what it could be used for. As you may know Apple recently, and rather quietly, stopped selling the iSight. What if the a new USB based iSight came out that could take advantage of all the 802.11n streaming goodness inside the Apple TV?
A newer iSight with better resolution, better low light sensitivity and ability to sit on top of your TV would give Apple the pieces for computerless living room video chats with Grandma in Toledo.
Since you'll need a high speed connection and 802.11n wireless router like the Airport Extreme (or an ethernet connection) to effectively use the Apple TV why not add a $199 - $249 high resolution iSight to your system and bypass sitting in front of the computer to video chat?
I could see Video Chat being added to the Apple TV menu via an update after the newer iSight is released.
Of course this would be for simple video chat - no file attachments, sending pictures, etc. And there would be setup issues, security issues for Apple to resolve, but this is the kind of stuff Apple does well in my opinion.