Maybe it has something to do with relative demand?
My guess would be that this is the unfortunate result of having to go through a middleman for digital distribution and losing all control over the terms ultimately reached with the digital retail company at the other end. EMusic's monthly subscription plan is by the number of downloads, and not by track length, so you could probably download several longform ambient albums for the price of, say, a digital Nick Lowe album. I don't know what the net royalty would be from the sale of a longform album on Emusic, but my guess is that would be less than what the artist would have received on Itunes.
Re Immersion's comments: I have paid for Robert Rich's mastering services and the licensing of Mark Mushet's professional images for the cover of my next CD. This comes directly out of my own pocket, and I hope to at least break "even" (and by that, I am not even thinking about any of my own time spent, which is considerable) on the CD through sales, physical and digital. I could not even hope for that to happen if everyone adopted Immersion's attitude that all digital music should be free for the taking.