One possible cause is the pricing: Kindle strongly encourages you to price books at most 9.99 and a publisher might want to price their eBook higher (so as not to undercut the print version).
Another reason is that it's not trivial to produce a good looking eBook, and some publishers might not have the technical know how.
Question for you: do you get all your books through Kindle store or do you also get PDFs and other .mobi downloaded from the net? Also, what's so bad about printed books?