I think bookstores face the problem that many other specialty stores do. The book market has gotten too top heavy, reliant on the "blockbuster". Like movies and music, it's only the top stuff that really sells (and thus makes them money).
They have to compete with the larger big box stores carrying the top stuff, and now on another front, e-books.
So no, it doesn't matter that whatever book Oprah and the NYTimes is pushing at the moment also comes with an ebook. They will still be competing with other sources, and they are always going to lose. And they've lost out on the niche market, just like the music and movie stores have, by their focus on the blockbuster to the exclusion of all else.