besides the US and English language and .epub format there are other languages, countries and formats - supported by 'nonames' (which are getting some name in places outside US) and not supported by big guys like Amazon...
Plus, there is folder management, some may like the way Kindle is handling its content, some would prefer a little more control over their own ebooks.
Plus, don't forget that e-Reading appeared a long time before Kindle did
Folks may have tons of stuff in their libraries, and this stuff couldn't be shown properly on Kindles or Nooks, while PocketBook or Onyx would show them pretty well.