So-called independent bookstores want us to support them. They argue they represent a locus of civility and literacy not available from the chains, and certainly not from online distributors like Amazon. I argue they are dooming themselves to irrelevancy and hurting the very business they purport to nurture in the way they do business. I won't suggest that all independent bookstores operate in the manner of places like Anderson's in Chicago or Book World (really a small chain,) but I suspect the economics as these small bookstores understand it drive them to behave in a way that is detrimental to the industry.
Generally, bookstores figure they need to get at least a 40% discount from the publisher (Anderson's asks for 50% much like Amazon). They also prefer to obtain their books from one of the large distributors, e.g. Baker & Taylor or Ingram. This puts small presses at a distinct disadvantage since they often can't afford large print runs or, to make things even more difficult, have resorted to Print-on-Demand, which has the advantage of not requiring much money up front and no warehouse or tax costs for inventory. Shipping can be done directly from the POD site. Unfortunately, the down-side of this practice is that the cost-per-book remains the same and the advantage of large print run lower costs doesn't apply except marginally. This means that often the best discount a small press can provide the bookstore is 20%. University presses find themselves often in the same conundrum and that's why you'll rarely find any university press books in bookstores except on college campuses. They are mostly offered direct to the consumer. Baker & Taylor will get them but at extremely reduced discounts (10% in my experience in a library) or with a surcharge.
I have seen authors published by small presses, books that have been well-received by the reading public and review community, be rejected by Anderson's (I hate to use them as the whipping boy, but I have more personal knowledge of their policies) because the publisher won’t give them more than 20%. This is at a conference where the author is being acknowledged. I happen to think that's foolish on their part since it seems to me 20% is better than 0%, but that's their business. They will sometimes offer the books on consignment if the author supplies them, but ask for a 50% discount which means the author has to absorb at least 30% assuming he/she can obtain them at 20% off. Book World, my closest independent book store will carry local authors only on consignment and not order from the publisher because they can't get the standard discount. In one instance, Book World would not even carry a local author on consignment (this author had been published by several legacy publishers) and would not order the book unless the small press provided a 40% discount, which, the publisher said they could not.
Note that Amazon carries all these books, often at a discount, and with Prime, delivers them for free in two days. It it any wonder then that readers and many small publishers are embracing ebooks with gusto?
Caveat: I speak from experience of thirty years as a librarian who made every effort to support local authors and while these experiences may not reflect the operations of all independent bookstores, I think the practices I described can be generalized.