Some suggestions for you to look at. If you have HDMI control set to ON turn it OFF (this may be why your TV is turning off your system) If you have ARC enabled also disable it unless you are sending a broadcast sound signal from your tv to your receiver and want to listen to it through the receiver. Also look to see if your Zone 2 has a "Fixed" or "Variable" setting for its output. If it does change it to Fixed and that way the Receiver will not control the volume level but the Apple tv will.
Yamaha CX-A5000, ATI AT 2007 Amp (7X200W), ATI AT 2004 Amp (4X200W)Klipsch RF 63's - Main, RB 61's - Front heights, RC-62 - Center, RS-62's - Surround, RS-52's - Rear Surround, 2 Rythmik DS-1510 DIY Subwoofers (With PEQ600XLR3 Amp) each connected with Antimode 8033S-II, Oppo BDP-95, MMF-7.1, Project Phono Box RS, XBox 360, XBox One