The Apple TV doesn't play a "subset" of Youtube videos as you describe it. The only Youtube videos the Apple TV doesn't play are those that the author of the video has enabled for only playing on the youtube website. If your mobile device can play the youtube video then so can the Apple TV. These types of videos are rare. Usually mostly official music videos.
But those are on Vevo and guess what? The free Vevo app on iOS devices support Airplay. And using your iOS device to browse and select content using multitouch and then Airplaying it to the Apple TV is better than having it built into the device itself because remotes aren't as good for browsing, searching, and selecting content as multitouch devices. Once the content is selected using Airplay, you can still use the remote for playback controls like volume, fastforward, rewind, etc which the remote is best for.
The problem with Roku is that it is very limited in high quality content like Hollywood Movies and TV shows, doesn't play your local content and rips, doesn't have Airplay, and the interface isn't as nice as the ATV. Pretty major downsides in comparison if you ask me.
Airplay by itself pretty much makes the Apple TV a no brainer purchase over the Roku. I just finished watching a 1080p .mkv video I had on my Mac using the Air Video app and Airplay from my iPhone. And I could do other things on my iPhone while it was Airplaying the video in HD to my big screen TV.
Can't do these kinds of things with the Roku. And with all the improvements and extra features available on the Apple TV with iOS 5 and the App Store likely just around the corner, the Apple TV makes a great choice that just keeps getting better and better.