Amazon has always understood that readers are the most relevant market and that's why they're in the position of power they're currently enjoying. Do they wield their big stick aggressively? Definitely. And so did B&N and Borders before them, and presumably whomever the boogeyman was prior to them were guilty of the same thing.
As anyone who's actually worked within a "vertical" knows, whether from a niche consumer or business-to-business angle (or, heaven help them, for a non-profit organization or political campaign), just because a subset of people share a common passion doesn't mean they're a single-minded group that can be engaged in one templated way. Every vertical that presents a viable business opportunity is going to have its own sub-communities and overlapping layers, with some often in direct opposition to others.
There are a number of challenges indie booksellers face—a shit economy being the biggest of them—and there are many that won't succeed, not because Amazon put them out of business but because THAT'S WHAT HAPPENS TO MOST BUSINESSES. There are many neighborhoods that simply can't (or won't) support a local bookstore, and that's perfectly normal, too.
If you're an author who has already been shook and sold your soul and firstborn to Jeff Bezos, I can see this seeming like a good short-term deal, but the potential repercussions are huge.
Much like Google didn't disintermediate big ad agencies via AdWords, nor TV networks or Hollywood studios via YouTube, but instead provided new channels for those who had no need for the Super Bowl, Amazon has done the same for authors who are better served with a scalpel than a mallet.
It reminds me of 2003, the year I started blogging, and how some people were able to attract large audiences for their writing, and the mainstream media scoffed that they would ever be taken seriously. Fast-forward, many of those early bloggers are now considered "real" journalists, some because they went to work for traditional media brands, others because they attracted a significant enough audience on their own that they couldn't be ignored.
Not quite one year to the day it was announced, Seth Godin is shutting The Domino Project down, offering the awkward explanation that "it was a project, not a lifelong commitment to being a publisher of books," instead of, perhaps, admitting that publishing is harder than it looks if you want to swim at the deep end of the trade pool in the middle of a dramatic transition, as he obliquely acknowledges in many of his noteworthy takeaways.