Perhaps Steve Jobs best explained what Apple did in his biography written by Walter Isaacson:

"We told the publishers, 'We'll go to the agency model, where you set the price, and we get our 30 percent," Jobs is quoted by Isaacson. "And yes, the customer pays a little more, but that's what you want anyway."

That's what some say is a smoking gun. Apple and the publishers have denied colluding on price but some of the publishers have engaged in settlement talks with the government. Apple has refused, according to reports.