Logitech Harmony software does not have an entry in its supported set of devices for Apple TV. But I managed to get it to work. There may be multiple ways of doing this. But this is how I got it to work: first add a Digital Music Server as a Device, and then add an Activity that informs the remote that you’ll be using your TV to control the sound. I’ve created a screencast of the steps.
Note: make sure that you’ve not paired your Apple TV with the Apple TV remote. If you do, then Apple TV will only respond to the remote that it was paired with.