I am having the same problem with all of my apple tv's (both Gen 1 and 2),
Since they updated iTunes (10.6.2 and 10.6.3) and the two latest Apple TV software updates, my apple tv connect when you start iTunes but after a while of inactivity none of my apple tv's will reconnect to iTunes. The only way the apple tv's will reconnect is after you restart iTunes.
I started syncing my Mac mini iTunes library to my Mac Book Pro iTunes library and then Home Sharing both computers thinking this way I will have two identical libraries incase one goes down I would have a live backup for seamless entertainment.
This worked for over a year, then once the iTunes 10.6.2 software was released it broke my setup (at the same time they released a update for the apple tv's also. Then they released iTunes 10.6.3 and another apple tv update but it still did not fix it.
I have tried just running one library at a time but it has no effect after a while of inactivity you have to restart iTunes for the apple tv's to reconnect.
I am runnning Lion on my Mac Book Pro and Snow Lep on my Mac Mini so it is not a OS issue (I believe).
I had a similar issue for months. I finally found a root cause. It may or may not be yours, but mine was so remote and random, I am decided to share in hopes it helps you shortcut your way to a solution.
Turns out I am having Wireless interference with my Wireless Soundbar/Subwoofer. I would loose connection or not be able to start playback on a movie for several hours, if ever... even with a locally stored movie on my imac to my ATV. I got a replacement ATV, moved my ATV (that worked find regardless of ethernet or wireless) from living room to the problematic bedroom area. That is when I discovered I must have a wireless issue in the bedroom.
So look around the room and see if you have a wireless anything that might be causing you an issue and turn it off. If your ATV starts working.... then you have found your root cause.