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Why do airlines choose routes? Not just about $
Justin Solomon | CNBC. The viral video depicting a passenger dragged off of a United Airlines plane has triggered outrage on Chinese social media. · CNBC

When an airline decides where and when to fly its planes, there's often a lot more at stake than just the bottom line.

The final choice of routes can be controversial, as United Continental (NYSE: UAL)'s recently ousted CEO discovered after allegations surfaced that the company initiated money-losing, nonstop service as a personal favor to a New York-area airport official.

But as the airline industry has sharply consolidated over the last decade, the battle for air service has become the subject of intense political and legal pressures from cities, local airports, politicians and businesses.

"Airlines play much broader, legal games that aren't so different. This stuff goes on all the time," said Seth Kaplan, managing partner at Airline Weekly. "There's a whole profession called air service development. People go out and hire consultants and do studies to make their case."

The haggling over air routes has intensified as the airline industry has consolidated, removed excess capacity and boosted profits. In the decade ended last year, the total number of seats available for domestic flights fell 6 percent. That boosted the average load factor—the percentage of full seats—from 76 percent to 84 percent, raising the revenue per passenger mile by 36 percent, according to the MIT Airline Data Project.

But as overall capacity shrank, cities were left to play musical chairs to see who would lose service when the music stopped. Much of the contraction reduced the number of short-haul flights—those under 500 miles—which hit many smaller airports harder than larger cities.

Cutting half-empty flights and closing down costly hubs have helped boost airline industry profits. Since posting an industrywide loss of $4.6 billion in 2008, airlines turned in a net profit of $16.4 billion last year and are expected to post a $29.3 billion profit this year, according to the International Air Transport Association.

Read More Cuts in air service stifling midsize cities

But the industry's drive to dump money-losing routes hasn't come without a fight.

Two years ago, the Justice Department sued to block the proposed merger of American and US Airways (NASDAQ: AAL), an action joined by attorneys general in states that faced service cuts. To settle the suit, the combined airline agreeed to keep operating hubs for three years at Kennedy International in New York; in Charlotte, North Carolina; Chicago; Los Angeles; Miami; Philadelphia and Phoenix. The airlines also agreed to keep their schedule of flights to small and midsize communities from Reagan National.