AnyDVD HD is required software to break the copy protection. If you want an ISO, there really isn't anything simpler than ripping to iso from anydvd. ToNMT is a nice program, but it's basically a front end for eac3to and tsmuxer. It downsamples HD audio to either DTS or AC3. It also only lets you keep one audio/video track, and doesn't allow you to keep subtitle tracks (how are you doing this?).
ToNMT basically just simplifies the ripping process for blu-ray, and forces things that you may not want (losing HD audio). I personally just do everything "manually" with TSMuxer/TSRemux and TS Splitter. I do actually use tonmt to identify the correct mpls on seamless branching files as it seems quicker to use that BDEdit.
You have to remember though that not everybody is streaming to an NMT like the Popcorn Hour. Some people are running an HTPC connected to their TV/Projector, mounting the BD iso and playing it back with PowerDVD. For those people, there is no need to strip the main movie from the BD. They just need a copy of the disc on their HDD/server.