As it stands right now, Amazon, Apple and Barnes & Noble decide exactly which digital books their stores will carry. Increasingly this seems to be books which do not reference other eBook sellers or are carried by other eBook sellers.
This puts eBooks in a decidedly different context than traditional books. I read an interesting article about this today at TheDominoProject.com. Founder Seth Godin talked a little about Apple rejecting his book because he had inserted a link to buy his book elsewhere.
Amazon has been doing the same thing, in a way, trying to coax authors into special promotions which allow their books to be only available at Amazon for a specific period of time. This seems like a good deal on the surface, but really just limits the audience you can potentially reach. Despite their level of promotion for some books, new authors face an uphill battle to promote their books and need as many eyes on their title as they can possibly get.
So, let's go back to eBook stores versus traditional book stores. Traditional book store will usually sell any title they can get their hands on. However, eBook sellers are also publishers, meaning they have a vested interest in selling certain titles over others.
It doesn't matter that this sends a chill through the eBook market in general. Because they are a business it is the bottom line which matters most and the less competition they have, the more they can funnel people to their eBooks rather than a competitor, the better it is for them.
However, because eBooks are easy to store, easy to distribute and easy to sell, it stands to reason that eventually a "store" will come along which does not discriminate based on the Ebook publisher used. It also seems likely this new store will itself be an eBook publisher, much like Smashwords does now, only to a much larger extent.
It also seems likely that as eBooks become more popular eReaders will themselves become less specialized and more of a catch-all product. This will be driven by the market. More people want eBooks, more eBooks will be offered. Although millions of eBooks are being sold, the market still has a great deal of growing left to do. The more the market grows the more powerful the buyers will become. Once the power belongs to the buyers, the rules will change yet again.