This question is asked by the SmartMoney blog and I must agree. I constantly question paying $12 for an eBook when the paperback is $6.99. Heck, the library is free.
Publishers seem to be just as baffled as the music industry was back in the days of Napster and files sharing. They are not sure what to do with those of us who want physical books in our hands as well as an eBook. We want to pay money and support the authors, but not be overcharged.
Will this ever get worked out? I hope so. Though we do have a current round of publishers being jerky about the Kindle Lending Library and limiting the amount of times and eBook can go out. Read about that here.