I assume the contract commits Apress to pay royalties to Mark based on their sales of the book's print edition. If they contractually agreed to pay royalties, they would be in breach of contract regardless of the licence under which Mark released his copyrighted content.

Notwithstanding the licence, Apress must have decided that they could make enough money on sales to justify the money they're paying to Mark.

Look at it this way: he might have released the book under a free document licence that another party could exploit, but he arguably wouldn't have written the book if not for his contract with Apress. So if they didn't agree to pay royalties, there would be no book to sell.