You know, I wonder if a small bookstore could help cover losses by offering classes on how to use the various versions of eBook readers? Charge a nominal fee for the class, then be sure to show the class visitors your website with links tied to your Affiliate program.
The one thing that small bookstores (like most SMALL business) have over the large ones is personal service. Get user loyalty going, and offer something different, and they might be able to keep the business going...
Most people new to e-readers will still want print books for a while. Speaking only for myself, it took about 5 years before I switched completely to digital versions (although part of that had to do with the minimal selection available back in 2002 when I first started buying eBooks).
I think in bigger cities, small bookstores have a harder time because B&N (or BAMM or whatever) will come in and "take over". But I don't know...it's funny to read in other threads about how B&N sold books at a discount, when I tend to think of them as more expensive that discount stores, where I always bought books (I never buy hardbacks, which might be where the difference is).