Interestingly, the decision PDF says that originally Amazon's $9.99 was not below wholesale cost. The publishers raised the wholesale cost above $9.99 thinking

Interestingly, the decision PDF says that originally Amazon's $9.99 was not below wholesale cost. The publishers raised the wholesale cost above $9.99 thinking it would force Amazon to raise their prices, but Amazon decided they would rather take a loss: "With a digital book discount, Amazon’s $9.99 price point roughly matched the wholesale price of many of its e-books. " ... "One of the strategies that they [publishers] employed was the elimination of the existing discount on wholesale prices of e-books. This meant that the wholesale price for e-books would equal the wholesale price for physical books, and as a result, the wholesale price that Amazon paid for an e-book would be set at several dollars above Amazon’s $9.99 price point. This tactic, however, failed to convince Amazon to change its pricing policies and it continued to sell many NYT Bestsellers as loss leaders at $9.99.9"