I too have used my Harmony One for my ATV1 for a couple of years, and as of this weekend, my new ATV2. Same command set. Just started working.
The workflow linked by Anthony above is good and works. I would repeat the caveat in that link that you must remember to UNPAIR your Apple Remote before you can PAIR the Harmony.
I also recommend setting the "Don't press Start" and "Don't press Stop" options when "starting or quiting an activity" in your Harmony One Device setup for the Apple TV Device.
Since the AppleTV uses a Play/Pause toggle and doesn't have a true Play and true Pause button, it's nearly freakin' impossible to do what you want it to do when you change activities. I prefer to start and stop the program material myself and not Harmony do that automatically.
That thread is VERY outdated. It's more current/accurate posts are on the last page, near the end. Or to simply sum up:
1. Add a new device, "Media Center PC"
2. Choose "Apple" as the mfg
3. Type in Apple TV (comes up as default)
4. Unpair existing Apple Remote
5. Pair Harmony Remote (by pressing Play I think)
Anthony...just ran across this while searching for info on fine-tuning my Harmony One to work with the latest Apple TV. The button customization in the thread you reference was very helpful, plus I added quite a few additional buttons.
This worked perfectly,, Asrai. But I did not have to unpair the existing remote. I just programmed it, as you stated, and the Harmony started working like a charm.