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.
It will be interesting to see what other publisher can successfully go the Marvel route; with a $2B+ worldwide box office already in for the Avengers' on-screen storyworld (one that still bizarrely lives in total isolation from the comics), I'm guessing several will make the attempt within the next 2-3 years. Two gaming franchises I think have some serious transmedia potential are Bethesda's The Elder Scrolls and Activision's Skylanders, though you might be surprised by which one I think has the most potential.
We are not anywhere near the digital future yet with comics. There is so much exciting ground to be staked out! We just need a new publisher, or a collective of coders, comic writers, and artists. I think the latter is more likely than the former.