When you allow a company like Amazon to control that much of the publishing business, you end up with some real problems. Among them, these are some very important ones:
* Amazon can dictate with their recommendation engine and promoted shelf what books you'll read. They can bury authors and whole topics and since they control so much of the market, these other books don't get a fighting chance to actually be seen, let alone bought. I'm not saying all books are the same. All stores prepare their shelves and exposure tables with care, but when you have multiple stores with different curators, the net effect of this is a variety of exposure. You can go to two indie stores on the same street and get a complete different experience in terms of what they recommend. Even though their recommendation engine does its best to place you in front of books that people like you enjoyed, that just create filter bubbles and echo chambers. It is good to be exposed to something else even if just to browse and decide to buy something different later.
* With it's quasi-monopoly, Amazon can dictate terms to publishers and authors alike. Royalties are always bad unless your self-publishing but Amazon can also extend that bad aspect of the business towards not only authors but publishers themselves. Negotiating with a company that owns the market is not really negotiating, it is compromising to unfair contracts.
* Have you tried buying an eBook from Amazon and adding it to a non-kindle device legally? What about DRM? Amazon vertical control of their eBook platform where they are the shop, the hardware supplier, and the only way to consume that content is much like Apple vertical control of iOS. New eReader companies have a hard time trying to survive the market because they can't read the books offered by the company that controls most of the market. It is quite refreshing to pick a device that supports ePubs and buying a non-DRM ePub from a publisher and just reading it without walled gardens.
* A big part of the bookshop experience is curation and the relationships you establish there if you're fortunate enough to be in near a shop that has events and fosters a local community. Don't get me wrong, books are products as well and selling them just like you sell shoes is a legitimate way of doing business, but it can be more than that. I've discovered many good books completely outside of my usual taste by going to events in bookshops and having interaction with real humans. If local bookshops die, this kind of experience dies with them.
So in the end it is not about using "bookshop" to avoid "Amazon", it is about keeping local shops alive so that the experiences and features they offer and that can't be replicated with a cold robotic Amazon shop, cease to exist.
There are many other problems with Amazon that goes beyond the book part of their business. Amazon is too big and companies working on that scale tend to be uncaring and treat their workers bad as you can't grow that large and not be playing the ROI and spreadsheets game of how much value can my capitalist practices can extract from both my clients and my workers.
On the other hand, local shops tend to more caring towards their clients and their workers. That is not an absolute and I've seen my fair share of horrible local shops as well, but for each one of those, there a many more shops run by people who actually love books and you can't have a good publishing industry if people who love books are no longer in every part of the supply chain. If all those people are in just half of the supply chain as authors, publishers and readers, but the commerce part becomes dominated by a single company, your overall industry quality will suffer IMHO.