Independent book stores have been falling to the big box stores for awhile now, but the recession and the rise of popular e-readers (iPad, Kindle) seems to be putting the final nail in the coffin. Here's a story out of Knoxville:
“When we opened, we knew there was a void—there wasn’t an independent new-books store in Knoxville,” McNabb says. “There were just the chains. And that’s where we came in. So that was early 2005, and at that point our main concerns were the chains and Amazon—but we thought we could live that way. And then late 2007, everything started changing.”
2007 is right about the time that e-readers started to pick up, and it was also the start of the recession - so I think it's been a nasty 1-2 punch to those outfits. The big box stores shouldn't get smug though; I can't recall the last time I visited one, and my wife and I read a lot. The Kindle store on the iPad is now our "go to" place.
My guess is that the big stores will hang on for a bit, but like the big record stores (remember those?), they're doomed. The thing is, a small independent store might be more helpful than one of the big box stores, but neither is as useful as "people who bought X also bought Y" - the Amazon recommendation engine. I've bought a ton of stuff that I never would have seen through that, and many of the books I've bought that way were self published, or from very small publishers. Which means that ultimately, this transition should be good for authors.