Make MKV is nice because all it does is rewrap the video (AVC, MPEG-2 or VC-1) and audio (extracted AC3 or DTS 5.1 cores) into an MKV container. Plays right in Plex or XBMC and will passthrough the audio by optical port.
While I agree that online sales is a substantial part of Apple's reasoning, I also think they have a legitimate beef with the licensing terms of Blu-ray, which includes kernel-level code and the ability to modify that code by a Blu-ray disc.
Apple will have to enable audio over DisplayPort for that. Optical doesn't have the bandwidth.
The Studios are pretty much run by a bunch of morons.