(I was half way through writing this before I realised I was merely enlarging on DeleyanLee's remarks, but I'm going to post anyway, I'm afraid.)
From a financial point of view this depends on how the author's royalties are paid. They may be paid as a percentage of the purchase price ('PP') or as a percentage of the publisher's receipts ('price received', or PR.) The price received by the publisher from the bookstore will be something like 50% of cover price or less, as the store of course buys from the publisher at a big discount.
It often happens that the bigger the bookstore, the bigger the discount they are able to negotiate; so that the author who is on a PR royalty finds that when her book is sold in Behemoth Books she gets much less per copy than her peers on PP royalties. Volume of books sold might well make up for this, of course.
PR royalties are often contractually triggered by high-discount sales, e.g. sales at a discount of over 50%. Book clubs, for example, might order big quantities of your book, but they'd get them at an 85% discount, which would mean you only make a measly 10% of 15%, i.e. 1.5% of the purchase price. The same might go for your export and coedition royalties. So probably the most profitable sales for the author will be those through the high street, brick and mortar outlets; the smaller and less tyrannical the better.
I'm interested in the argument that you should buy from chain bookstores because they have more influence over the market. They wouldn't necessarily make more money per sale than for a sale through an independent bookseller. I can see how it helps from the point of view of building a good sales record with an important vendor, which could mean they would order more copies of the next book by the same author. However I think we'd all be better off with more independents. Any large chain store I go into has almost the identical range of books - centralised buying has squeezed out much of the opportunity for taking a punt on something risky or exotic; and the whip hand for the stores inevitably means they drive harder bargains, and publishers and authors take less money home. For these reasons and more I can think of a few buyers for big stores who have made themselves extremely unpopular in the industry...
So my instinct is: support your local independent bookseller.