The superstore book store model is a money loser. Before Borders went belly up, its Waldenbooks stores were actually losing less than its superstores. And publishers are the ones making the most from ebooks. Last I knew, most, if not all publishers, were charging e- and retailers the same price for the electronic editions that they charge for the dead trees. Plus, the increase in transpo, warehousing, other costs are really doing a squeeze on margins for book retailers. Changes in publishing are also taking place. My bet is that, other than indie booksellers, the only big guys who’ll make a profit selling dead tree books will use a convenience book store model, kinda like what Waldenbooks and B. Dalton used to do.
Also, Borders burned a lot of companies on their way out. B&N’s probably paying for that, too.
The publishers' business model is unsustainable in a time where authors can put their books up directly on Amazon.
One of my favorite bloggers (freeper "wretchard") sells his novels that way. Freeper Travis McGee sells his books from Amazon as well as from his own website, etc.
Big publishers used to be needed, because big printing presses used to be needed. In the ebook era, what's needed is a good editor (who can be retained freelance), plus a way to get people interested in your writing style.
Baen Books (science fiction publishers) has a nice setup where you can read the first few chapters of a book online, and then decide whether to buy.