So, if a publisher gives even a 50% discount for .pdf products over a print version, said publisher is still making quite a bit more money off of the .pdf vs. a traditionally printed and distributed product. And while a system like RPGNow might charge a percentage to sell a book (I looked into it once, but I forget how much it is, exactly) it's nowhere near the amount the publisher loses in the traditional dead-tree distribution model.
I thought OneBookShelf (RPGNow and DrivethruRPG) took in the region of 30-35%. When the merger took place, I thought that was the number I saw mentioned, which was why some publishers left to other sites. So if WotC is giving 30% off, and OBS take 30% off what's remaining, it's not far off from the retail dead tree profit.
Pinotage