Under the traditional book-selling model, retailers like B&N, Amazon, and others could get 50% or more of the revenue from the sale of a book. Under Apple's "agency model", they get 30%. The traditional model is retailer-centric. Apple's model is publisher-centric.
This upsets the US Justice Department. Under the old model, the retailer set the price and so could sell the book at any price they wanted, even at a loss. Under Apple's model, the publisher sets the price, so there's no retailer discount.