When the chains took over, the independents could survive by becoming niche. But the internet has killed that avenue. There just isn't a good viable model for an independent bookstore. Same thing happened to record stores. Which is sad, really. Browsing the aisles of a unique bookstore (or record store) is something an ipad experience just can't match.
The owner of Murder By The Book went to a Borders to buy 40 copies of the new Jim Butcher Dresden Files book. Are publishers abandoning independent bookstores as well?