The architecture of the internet is actually outdated. I mean, it may take a few years for people to realize this, but the fact that we have to go to a specific web domain, which is tied to specific hardware or private network, in order to search for things like Kindle books (or Google for practically everything else), is creating monopolies that aren't beneficial to consumers or retailers.
Usually people dismiss that idea out of hand in the context of e-commerce because they don't understand how peer-to-peer networking can be secure or private. But in fact it can be, it has to be, and it will be. Its going to take everyone a little while to figure that out though.
There's value to some creators in having a marketplace in order to get exposure and to provide a convenient browsing experience for customers. Independent musicians who give away their music for free are often grouped into netlabels so that people can find them and discover other works that are somehow related.
A large portion of applications on the Mac App store were and are available directly from the creators, but plenty of authors elected for a presence there. More independent models, such as Cydia and Ubuntu Software Center still take a cut of sales.
Review sites might be one way around the issue-- say, if it was possible to browse GoodReads and every book you were interested in had a link to whatever distribution method the author chose. But then, if GoodReads was the go to site for books, it might start charging a cut too, or prioritizing sponsored links.
As far as e-books go - the problem is 'reach'. Pulley and Shopify just don't have the reach that Amazon does. Authors are still trying to figure out the best ways to monetize without going through publishers and it will take time for their thinking, and Amazon's competitors, to mature.
We tolerate middle men because it's easier for a single human with a singular vision to create an easily searchable marketplace of creators' content than it is for the creators themselves to come together in a cooperative and form it themselves.
TLDR; Humans are good at following leaders and complaining about results rather than working together and leading themselves.
(Presidential elections are a perfect example of this)