PDF is used by a lot of publishers because it's what they send to the printers so they don't have to do anything extra to release the ebook. (For freebie promos, they tend to leave in the hideous production metadata and sometimes even have the printer's crop marks.)

My first experiences with ebooks were mostly Fictionwise multiformats, and for most of the time I've dealt with ebooks, I've had Acrobat Pro with a cluster of shiny plugins, so I can convert & reformat PDFs.

I've tried a tiny handful of ebooks with DRM, fixed formats that I couldn't adjust the layouts or fonts, and I would've given up entirely if that was my first exposure to them.