As an author, I can tell you that Amazon and their eBook pricing means more money (overall) for Authors. Maybe not for the "best seller"s who don't actually sell many books, but their publishing house prints lots of them and sends them out to stores, so while they end up on the bargain rack or destroyed, they still make the NY Times list based on the lay-down. Yeah, the authors people don't actually want to read will ultimately make less money, but the real authors that people like and want to buy from will make a lot more.
There is currently a battle going on in the industry between the special favorites of the big 6 publishing houses and the midlisters and independents. There are very few authors who can get a reasonable deal out of one of the publishing houses. Everyone else is getting contracts which require them to sign away their works forever, sign away any future works in the same genre, sign away all electronic rights, etc... for a $5K advance on a one or two book contract.
The midlisters and indies are running to ebooks and small publishing houses as fast as they can. It's not a mystery why. Amazon will pay 70% on an ebook. A publisher will typically pay maybe 15% (on poorly documented bookscan sales numbers, even on eBooks, which should be exact!) Where they used to purcahse only limited publication rights, which expired after they took the book out of print, now they want contracts where the author will never get their book back, even if the publishing house isn't actually doing anything with it.
If you are a well-known celebrity, or you sell millions of copies, then a big 6 publisher may work with you on somewhat fair terms. Otherwise, they won't edit you (it's gotten much worse over the last few years), they won't market you and they'll barely make sure your latest book stays on store shelves for a month.
The big 6 publishers are not only an issue in terms of IP rights and author payments, but they are also a very bad gatekeeper. Ever wonder why so many old SF authors stopped publishing and much of what is out there now is crap? It's because they're being picked by a publishing house with a NY "editor" who probably doesn't even like SF. They literally drove popular authors (who wrote what people actually wanted to read) out of the business. If an author sold too much (i.e. more than the editor projected), did they reprint and push the book? No, they'd keep the same print run and just stop publishing it when it hit the number projected as the max, usually tiny. Baen was the only real exception of any size in the industry. Jim Baen also did eBooks right from the start (gave old ones away in order to promote newer books in the same series/by the same author). That's all just starting to turn around because of Amazon, on-demand publishing and eBooks. Old famous authors are even starting to put out the books their publishing house stopped selling, or that they couldn't get published in the first place because it wasn't the editor's latest fad.
Also, the big 6 publishing houses have a massively left-leaning bias. They've spent decades now killing the sales numbers of entire genres because the authors were required to toe the line of the latest politically correct movement. You can date books in some genres by the issues and characters the editors required. Many books that adults like have been pushed into YA categories, just because if it it's not "edgy" enough, the NY editors don't want to buy it. Forget about what will sell, they buy what they'll want to tell their NY publishing friends about at the next cocktail party.
Scalzi is the poster-child cheerleader for the big 6 publishing houses. He's on the "inside" of the publishing establishment and does everything he can to defend them. He could care less about SF authors, just about his publishing buddies.
You want the real scoop on Amazon and Authors? Go look at Mad Genius Club, or According to Hoyt.