Two reasons: Amazon, Apple, B&N, and others all want a huge cut of the pie yet also 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 actually more important: Kindle, Nook, and most other eReaders tend to use file formats that aren't very well suited to complex, graphic-intensive works. Their app stores tend to require the use of those special file formats. The tools for creating said works the way they want them to appear in their stores 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. This is slowly changing, but still requires specialized tools. I use a special set of fonts in my books that recreate Nikon’s icons directly, for instance. epub doesn’t allow such font use.
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.