Henry Harteveldt, co-founder Atmosphere Research Group, said the airlines and travel sites have "a very, very dysfunctional business relationship." The travel sites treat all flights equally. Price is the only differentiator.

"The online travel agencies either won't or can't talk about how an airline might have Wi-Fi on a plane or extra legroom seats available," he said.

The online agencies say they provide travelers with several advantages, including comparison shopping and the ability to mix and match airlines for a single trip.

Bing: Search hotels for your next trip

"That's something you can't do on an airline's site," said Dara Khosrowshahi, president and CEO of Expedia, Inc.

Simon Bramely, vice president of transportation and lodging for Travelocity, part of Sabre Holdings, noted that "the flight is one element of the trip." He said online travel agencies can save travelers hassle and money by creating packages that include hotel rooms and car rentals.

The battle is not new. Southwest Airlines Co. was a pioneer in cutting out the middleman. The airline does not list its fares on third party sites. That means travelers have to search both southwest.com and then elsewhere to compare fares. Southwest hopes fliers will never make it to another site.

"We think we can have better control over the customer experience by dealing directly with them," said Southwest spokesman Chris Mainz.

Most of the big carriers have remained quiet. American Airlines, part of AMR Corp., was the exception. In December 2010, American cut off Orbitz Worldwide, Inc. from displaying its fares and selling its tickets to protest the commissions and the failure to displays extras like seat upgrades. The site had been selling about 3 percent of the airline's overall tickets. Expedia joined the fight by making American's fares harder to find. All sides eventually settled their disputes.

Frontier, part of Republic Airways Holdings Inc., is making its changes specifically to cut the commissions.

A four-segment itinerary -- say a roundtrip flight from Sioux Falls, S.D., to Phoenix connecting in Denver each way -- booked directly through Frontier costs the airline $1.60 to process. That same itinerary booked through an online travel agent costs Frontier $20 to $26, depending on which website the ticket is booked on, according to Shurz.

Those commissions add up: Shurz said Frontier spends about $55 million to 60 million annually on distribution fees. In the first half of 2012, 42 percent of Frontier's $713 million in revenue came through tickets sold directly with the airline. Shurz hopes to increase that figure to 65 percent in a few years, cutting expenses in the process.