Two reasons: Amazon, Apple, B&N, and others all want a huge cut of the pie, yet do no additional work while wanting to force prices to very low levels. For small, niche works like mine, it doesn't make a lot of sense to use these online stores because sales would have to be insanely greater to generate the same revenues.
Without a reasonable revenue stream, I cannot afford to buy, test, document, and support 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 non-fiction works. This is slowly changing—my Zf and Zfc books are an attempt to walk the ePub plank without dumbing them down—but still requires specialized tools to create. I use a special set of fonts I created in my Complete Guide books to show Nikon’s icons directly, for instance. Mobi doesn’t really allow such font use, and ePub only recently added it.
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 my Complete Guides in the PDF format. That said, most eReaders today, including the iPads, Kindles, and Nooks, can display a 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.
