Software update to the rescue!
The latest update for the ATV seems to let you program almost any remote for it. There's a new option that lets you step through each of the common functions (left, right, select, play, fast-forward, etc.) -- for each one, it tells you to press the button on your remote that you want to perform that action. It couldn't have really been any easier, and now we get to use our TV remote to control our ATV.
Way to go, Apple!