Wouldn't it be easier to use Mac The Ripper 4.0 (MTR) to rip the DVDs? Handbrake can't deal with the copy protection on DVDs, can it?
And then after ripping using MTR - using the default option to create VIDEO_TS folders instead of the ISO option - you could use XBMC on the Apple TV to view the ripped DVDs, which would include all the DVD extras, audio tracks, subtitles, etc.
The downside being that the VIDEO_TS rip results in big files. If you have the time, then you could then go back and use Handbrake to transcode the individual files (the main full movie, specific extras, or episodes of shows) into smaller, Apple TV-friendly files, so you can just use Apple TV/iTunes to manage and view the files and not have to worry about ATV hacks like XBMC/Boxee/Plex/ATVflash.
I currently use MTR to manage my DVD backups/rips, and VLC as my viewer. I've been experimenting with XBMC/Boxee/Plex, which offer cooler interfaces and (sometimes good, sometimes bad) auto-tagging of movie and TV files (regrettably they don't seem to recognize meta tags, so I've been skipping the MetaX tagging step). I'm thinking about getting an Apple TV soon, so I'm curious about what the easiest and quickest steps really are for getting my movies onto the Apple TV, so I can stop using my DVD player.
For me, MTR to VIDEO_TOS (and playing the files with VLC) has been the best option for managing the DVD media on my iMac and Macbook -- I've been doing this for a few years with various versions of MTR and VLC, and it's fast and simple.
But the cool-looking interface provided by the (still buggy) XBMC/Boxee/etc. programs are compelling, and I really want to start getting my movie library onto my TV via an Apple TV if it's not too much of a hassle. I know that Mac Mini is what I really need to do this easily (as discussed by others in many posts on the MacRumors forum), but the Mac Mini seems like overkill for my purposes (e.g., more $$ than I'd like to spend, and still not an out-of-box solution anyway, in terms of syncing media between computers).
I also bought a DLA media server, but it was a very disappointing experience.
Suggestions?