Part of this is intrinsic to the industry: just like with movies and music, the writer(s)/actor(s)/artist(s) is/are the source of the desired material, so regardless of whose label is affixed to those names, consumers will make their purchases based principally on the artists involved. As a culture, we care about Johnny Depp more than Lionsgate, Jay-Z more than Def Jam Recordings, and Suzanne Collins more than Scholastic.
Another part of it, however, is due to publishers' treatment of their own brands. Many include their logos on the spines and back covers of their books, but never the front (Penguin Classics is a notable exception), and publishers with myriad subdivisions and imprints further confuse consumers by including those logos but not the logo of the parent company.
How many of you knew that Dutton, Gotham, Prentice Hall, Riverhead, and Viking were all part of Penguin? That Knopf, Crown, and Ballantine are all Random House (and that those groups contain their own smaller imprints)? That Grand Central (with its imprint, Twelve) is Hachette's, as is Little, Brown & Co.? I could go on, but you get the point.
I think a significant problem for publishers in the industry today is a lack of brand consolidation. A lot of it is because individual imprints have their own specialties and want to maintain their identities apart from their parent publisher: Threshold (Simon & Schuster) specializes in conservative politics and nonfiction, Tor (Macmillan) in science fiction and fantasy, &c. This is all fine and good—or at least, it has been—but with companies like Amazon and Barnes & Noble beginning to dominate the market, publishers will have to change the way they play the game.
As Sarah Lacy at TechCrunch notes, Amazon is preparing to take over the role of publisher in the world of tomorrow. And in that hypothetical world, I think Amazon's name would be just as important as most of its authors'.
Unless traditional publishers can reinforce their names and reaffirm their relevance over the next five years, I don't see why anyone will prefer a Random House book or a Penguin book over an Amazon/Kindle book. Authors will always be major brands in publishing, but I think publishers will need to increase their visibility as well. If they continue to bank on running the show from behind the scenes, it's my opinion that it will be to their long-term detriment.