Two reasons: Amazon, Apple, B&N, and others all want a huge cut of the pie yet want to force prices to very low levels. For small, niche works like mine, it doesn't make a lot of sense to use these stores because sales would have to be insanely greater to generate the same revenues. Without a reasonable revenue stream, I cannot afford to buy and test the equipment in the depth I do in generating my works.
But the second reason is more important: Kindle, Nook, and most other eReaders use file formats that aren't very well suited to complex, graphic-intensive works. The tools for creating said works the way they want them are also still very crude. While .epub, .mobi, and .azw file formats work well for novels and other books that are mostly text with relatively little formatting needs, they work far less well for complex works.
My Complete Guides have a lot of sections, graphics, tables, step-by-step instructions, and other things that just don't play well in the native eReader formats. That's one reason why I produce them in PDF format. That said, most eReaders today, including the iPads, Kindles, and Nooks, can display PDF perfectly fine (as long as the PDF was formatted with them in mind, which I do). Curiously, Amazon and B&N don't want independent publishers giving them PDF files, so the point is moot: I sell my products independently.