Note: I'm not taking any position on whether the EU regulators were correct or not. I'm not familiar with either EU antitrust law or with how Google shopping actually works.
You go to Amazon because you want to see what Amazon is selling. When Amazon in response to that shows you products they are selling, it is hard to see how that could raise antitrust issues, no matter how big Amazon is.
You go to Google's search page because you want to search the web. Google responds by showing you the hits on the web, AND by showing you things they think you might want to buy through their shopping service. They are using one line of business to give a boost to a different line of business. That's the kind of thing that does draw antitrust scrutiny.
An analogous situation with Amazon would be, perhaps, if when you searched for books on Apache or MySQL or other server software, they also showed you deals on AWS hosting.
An analogous situation with Amazon would be if they wrote and published their own books and started putting those at the top of all the search results.
For one, Amazon is not that dominant in the first place (Google has 80% of the world's searches, Amazon has nowhere near 80% of e-commerce -- estimated to get to around 20% in 2016).
Second, they can't really use their (non)dominance in Shopping to sell kindle fires. At most, they can promote them to their users. Most of which haven't bought one, and wont buy one, according to number of Amazon users vs estimated Kindle Fire sales numbers.
You go to Amazon because you want to see what Amazon is selling. When Amazon in response to that shows you products they are selling, it is hard to see how that could raise antitrust issues, no matter how big Amazon is.
You go to Google's search page because you want to search the web. Google responds by showing you the hits on the web, AND by showing you things they think you might want to buy through their shopping service. They are using one line of business to give a boost to a different line of business. That's the kind of thing that does draw antitrust scrutiny.
An analogous situation with Amazon would be, perhaps, if when you searched for books on Apache or MySQL or other server software, they also showed you deals on AWS hosting.