It's the MFN clause!
it's hard to see how a company with a mere 10% market share of ebook sales at best was the dangerous one in breach of anti-trust regulations, while Amazon—who have over 90%—were not.
You're missing the whole picture. The "Amazon is the dominant player" card is what Apple tried to use to justify their actions. But in reality, they were involved in a price-fixing conspiracy that gave plausible deniability to both parties thanks to how the contracts were made. The key was in the following things:
Publishers were giving Apple the books under the "agency" model, which unlike the "wholesale" model the price per book is fixed by the publisher. Apple gets to set the percentage they keep, which they put at 30%. Up till here it seems to be OK, except:
Apple added a "Most Favoured Nation" clause. Publishers that sell to Apple can't offer lower prices to other vendors, like Amazon/Kindle. Thus this clause forces everyone else to a) switch to the agency model, even if they don't want, and b) sell at the price point that the publisher has fixed. Oh, but the publishers could just point and say "oh but Apple is selling them at that price and we can't offer 'em cheaper due to our MFN contract!". But the truth is that the e-book market as a whole had a massive price hike after Apple & Co. made their deal; it was getting so stupid that paper books ended up being cheaper in some cases! And that's why Apple lost; the price hike was so noticeable that it was successfully proven in court.