Actually, he's not due anything back. Per the T&C of the MasterCard (the bolding is mine):

"The applicable checked baggage fee will be automatically waived when the primary cardmember's OnePass® account number is listed in their reservation. In the event that it is not automatically waived, the primary cardmember should present their active Continental Airlines Chase credit or debit card to an agent. Fees will be waived at the time of travel; no refunds or credits will be issued after travel has been completed."

However, a question comes from this (not relating to this OP's problem, though): I have a CO World MasterCard & have one for my wife as well. If she travels without me & shows the agent her card, how will they know that she is not the primary member? Will the agent really call Chase to figure out if she's a primary or secondary member, or will they just waive the fees?