Some people have questioned whether the publishers are struggling. Mark Cooper, research director at the Consumer Federation of America, suggested the e-book pricing agreements likely went directly to profits in a sent earlier this week.

Some of the publishers in the DOJ lawsuit are private companies, so it's difficult to discern what financial shape they are in. But Simon & Schuster is a division of CBS, a public company. In 2011, Simon & Schuster had revenue of $787 million, falling each year from $857.7 million in 2008.

The DOJ lawsuit may force a change in the publishing industry, Weiner said. In addition, the lawsuit may force Apple to rethink its commitment to selling consumer e-books, instead of focusing on textbooks, he added.

"Apple may, at some point, decide that this is not worth the hassle," he said.

The DOJ's settlement with three of the publishers will also shake up the publishing industry, added Kellie Lerner, an antitrust lawyer with the New York-based Labaton Sucharow law firm. The DOJ will enforce some provisions of the settlement for up to five years, making it nearly impossible for other publishers to set e-book prices, she said.