The whole Apple situation is a good deal more complex and basically is a matter of several giants fighting it out to shape the future direction of ebook distribution.
There was (and largely still is) only one game in town; Amazon and the Kindle. The publishers joined forces with Apple to try to break that monopoly. To do so they broke anti-trust laws and, frankly, opted into a model that was at least no better for consumer, likely worse in the short term.
This piece (from an author) on Amazon's ebook strategy outlines why they tried to attack it. The short version (all terms defined at length in the piece);
And the peculiar evil genius of Amazon is that Amazon seems to be trying to simultaneously establish a wholesale monopsony and a retail monopoly in the ebook sector.
You're probably familiar with predatory pricing. A big box retailer moves into a small town with a variety of local grocery and supermarket stores. They stock a huge range of products and hold constant promotions, often dumping goods at or below their wholesale price. This draws customers away from the local incumbents, who can't compete and who go bust. Of course the big box retailer can't keep up the dumping forever, but if losing a few million dollars is the price of driving all the local competitors out of business, then they will have many years of profits drawn from a captive market to recoup the investment. (Meanwhile, helpful laws allow them to write down the losses on this store as a loss against tax, but that's just the icing on the cake.) Once the big box store has killed off every competiting mom'n'pop store within a 50-mile radius, where else are people going to shop?
Amazon has the potential to be like that predatory big box retailer on a global scale. And it's well on the way to doing so in the ebook sector.
Amazon had/has been treating ebooks and Kindles as a loss-leader for a while. All the while they had been including (publisher mandated) DRM on those books they sold, locking readers into their formats and their readers into the forseeable future. If you are already invested in one reader type, one file format, one library, when it comes time to upgrade your reader you can't really afford to shop around. Buying that awesome new B&N reader to replace a Kindle means being unable to use your Kindle books on it, surrendering the use of that collection you have been building (obviously DRM cracks not included).
This meant, when it came to ebooks, customers were getting locked into an Amazon monopoly while the sellers were effectively only selling ebooks to Amazon in a monopsony. Amazon could dictate everything about the market. They had started dictating terms that effectively made them a sub-publisher of the ebooks, sublicensing the book to be sold as a Kindle ebook rather than buying each ebook individually from the retailer. This basically pushed publishers out of the retail chain completely. They still made money from ebooks, but that market was fully dictated by Amazon's terms and they couldn't do a damned thing about it. This is ignoring the areas where Amazon have explicitly become a publisher themselves (most obvious being Audible for audio-books).
The Apple agreement was about an agency model of ebook sales.
An older piece outlining the basics (worth noting that was two years before the piece linked above and interesting to watch how his views shifted somewhat). It was always about breaking Amazon's retail model. It did so in a grossly non-competitive manner. The four chains;
Traditional: author -> publisher -> wholesaler -> bookstore -> consumer
Amazon traditional: author -> publisher -> Amazon -> consumer
Kindle/Audible: author -> Amazon -> consumer
Agency: author -> publisher -> fixed-price distributor -> consumer
The Agency model kept the publishers in the supply chain, removed the traditional wholesaler/bookstore distinction while also denying the distributor the obscene power that Amazon was grabbing.
After the lawsuit and the publishers backed down (somewhat) on the non-competitive aspects more changes were announced. The biggest has been the steady move of Macmillan away from DRM. This one move helps simply by stopping Amazon from locking (non-DRM cracking) customers into their format and readers. Someone who has a massive Kindle library of non-DRMed books can simply convert those to a new format if someone offers them a better reader. Suddenly Amazon has to remain competitive into the future, not just lock people into their marketplace and then do what the fuck they like (we can call this the Microsoft model).
As far as the agency model being bad for consumers, it's probably worth noting that both
theoretically and
practically the agency model generates lower prices than the wholesale model. The Amazon lower prices were loss-leader discounted prices, not reflections of a more efficient model.