The Apple TV is smarter than that. You actually teach the Apple TV to use whatever remote control you want to use. It's kind of nice to have a home electronic that's smarter than a remote control. It can even use the remote that came with your television, cable box, or DVD player. Here's how to do it.
Go to the Settings menu, select General, and then Remote. Choose the Learn Remote option. Make sure the remote you're using isn't already controlling something else (like "Television.") On the Apple TV, choose Start. On the Apple TV screen, the Up button will become highlighted. Press the button on the remote control you'd like to use for Up. And then continue down the rest of the controls.
Setting up a new remote to work with the Apple TV really couldn't be much easier.