Put Apple to the side for the moment and just look at the publishers. Did they conspire? I think it is obvious that they did.
At the time of the agency switch it was obvious something fishy was going on with the whole Amazon v MacMillan "buy button" battle. The DoJ's investigation uncovered plenty of evidence about what that was: a conspiracy among publishers to force Amazon to the agency model. And all the publishers settled before getting to trial, which certainly supports the strength of the DoJ's evidence and case.
Now consider a publisher conspiracy. The DoJ's argument against Apple is that they were the enforcer that made the publisher conspiracy possible. You may agree or disagree with the judge about whether or not the evidence supports that argument, but it is a serious, carefully-thought-out line of logic either way.
At the time of the agency switch it was obvious something fishy was going on with the whole Amazon v MacMillan "buy button" battle. The DoJ's investigation uncovered plenty of evidence about what that was: a conspiracy among publishers to force Amazon to the agency model. And all the publishers settled before getting to trial, which certainly supports the strength of the DoJ's evidence and case.
Now consider a publisher conspiracy. The DoJ's argument against Apple is that they were the enforcer that made the publisher conspiracy possible. You may agree or disagree with the judge about whether or not the evidence supports that argument, but it is a serious, carefully-thought-out line of logic either way.