I don't know anything about these independent bookstores making money hand over fist. I haven't audited the local independent bookstores and music stores, so I don't know their financial details, but they don't seem any different than any other business. They continue to employ people and continue to stay open, do they must be doing ok. Most people would call that thriving.
Just depends on your standard of living I guess. Most small business owners are upper lower class to lower middle class and barely getting buy each month. I don't call that thriving, that's just surviving (for both the store and the owner).
The ones that are thriving are the ones that area always busy, not the ones that just sell a few books a day to fans of a certain niche. The ones doing very well financially are the ones that always have people in them spending money on books, coffee etc. That's all I'm saying by "thriving."