Because consumers were out with pitchforks over books being higher than $9.99 like Amazon was doing it and screaming at the various governments to do something about it.
Ruling against Apple and making them and the publishers fall on swords gives the DOJ etc the power to look like they are listening to the consumers and protecting them from big bad companies. Never mind that we are taking about a non essential item for the most part and consumers could just not buy until the publishers were forced to lower costs.
See, the problem I have with your argument is that it's based upon the assumption that Amazon WAS doing wrong, and the publishers/Apple came together as a means to combat it.
Let's assume they were. Amazon did have a market monopoly, and were abusing their position with wild abandon. The publishers banded together to do something about it. But rather than using their combined power to take it in front of the DoJ, they came to a mutual agreement to fix prices, and force the agency model upon the entire industry as a whole. The end result being that the power to set prices was taken from retailers entirely, and controlled by the publishers themselves.
And this is absolute fact. During the time all this was going on, there were no book sales. No price competition among the resellers. No reason to choose one outlet over another. All resellers were turned into fronts for the publishers, and since there was absolutely zero competition amongst them, prices were set across the board. Amazon couldn't undercut their hardcover sales with cheaper ebooks anymore. They were comfortable.
This is especially true of Apple, who gained the largest, most solid foothold in the ebook business during that time by riding the momentum they created with the iPad. Amazon was only able to keep a majority share due to the fact they still had a ton of current Kindle owners to fall back on. Apple didn't have to compete with Amazon toe to toe. The publishers did it for them by hobbling Amazon the moment the iPad was released.
When looked at from this perspective, it seems rather suspicious, doesn't it? When taken with the evidence that the publishers worked together behind the scenes to fix prices, with Apple darting around somewhere behind the scenes, it becomes outright damning.
...but they were competing with an established monopoly, right? They had to do what they had to do just to compete. See, the problem is, they went after an illegal, damaging monopoly by creating another illegal, equally damaging monopoly. They colluded to potentially kneecap one business, and allow another, one directly involved in said collusion, to potentially thrive.
And if you believe Amazon were a little shady, but otherwise working within legal boundaries that still allowed for competition, then it becomes even worse.
You don't necessarily have to like what Amazon does, but the very reasons you don't like Amazon should be the very reasons you don't like what Apple and the publishers had done.
No matter how you look at it, everyone involved in the collusion issue were in the wrong.
