We still have several indy bookshops, used and new, in the small town where I live, but that's because we're too small to support a B&N/Borders/whatever chain store. When the chains come in, that's when the indy's tend to die out (except in college towns, where they seem to hang on quite well).
Ebooks are still only about 1% of the book market - they're an easy target to blame, but not an accurate one.
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