Unplug the Appletv hdmi cable from your tv. Power cycle. Plug it back in and power on. You may have to go through the device set up on the tv again. HDMI-cec is one of the buggiest protocols for n existence. Sometimes it just breaks for no reason.
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Also powercycle the TV, that solved this for me.
Can you use the ATV remote to get into the Settings and try to re-learn your Samsung remote?
Settings > Remotes and Devices > Learn Remote
I am not talking about IR remote control, but HDMI-CEC control. I tried this now and the Apple TV can learn the remote, but there is a mild annoyance that the TV is showing a warning on every keypress covering half of the screen, that this keypress is not supported on the current mode. It looks like that both the tv and the Apple TV is trying to interpret the IR codes. Also I cannot teach the playback controls because I dont have all the rew/fwd, prev/next track beginning/end buttons on the remote, only play pause stop rew/fwd.
This is standard. Mine worked great when I got a new samsung tv. Then it just stopped after an updated version. Everything else works with it except the AppleTV.