Incentives matter. Five years ago, the Department of Transportation published a well-meaning rule: if passengers are kept on the tarmac, the airlines are assessed a fine of $27,500 per passenger. Unsurprisingly, with such a prohibitive fine, the incidence of airlines keeping passengers on the tarmac for three hours has plummeted.

U.S. airlines reported 207 tarmac delays of three hours or more (of over 25 million scheduled flights) for the five years after 2010, according to DOT data. In comparison, U.S. airlines reported 5,618 long tarmac delays (of more than 29 million scheduled flights) for the five years before 2010. (See chart below.)

So how did the airlines deal with this new rule?A new study by Dartmouth and MIT found that instead of letting passengers linger on the tarmac, instead they simply cancelled the flights and rebooked the passengers to fly home later.

The study found that five-year-old rules established by the U.S. Department of Transportation decreased tarmac delays, especially long ones, but it had an unintended effect of causing other passenger delays mainly because flight cancellations rose and passengers required rebooking. …

“It’s good that the rules saved time on the tarmac, which is really painful to travelers, but it causes extra delays that are three times as long,” said Vikrant Vaze, an assistant professor at Dartmouth’s Thayer School of Engineering.

So which is worse? Sitting on the tarmac for three-plus hours, or scrambling back into the terminal to get rebooked? My experience–the former, by a lot. Have you ever been on a flight that was cancelled? What happens is immediately 200 people storm the customer service desk, fighting for one of the few remaining standby seats available. (Passenger with higher status prevail over those who scream louder). If you have a connection? Forget about it. There’s no way you’ll make it. Once I got stuck in Phoenix for the night because my connecting flight landed an hour late–I missed the last flight of the night to Houston by about 3 minutes. It was always my sense that a delayed flight is better than trying to catch a later flight.

The study offers a series of suggestions to make things less bad.

The researchers think “a better balance between the conflicting objectives of reducing the frequency of long tarmac times and reducing total passenger delays” can be reached with a few tweaks to the existing rules, Vaze said.

Here are their suggestions:

* Change the tarmac time limit to 3.5 hours.

* Apply the tarmac limit rule to only flights with planned departure times before 5 p.m.

“This adverse side-effect from the rule gets progressively worse later in the day because there are fewer flights to be rebooked on and people may have to stay overnight in a hotel,” Vaze said. “The sweet spot seemed to be 5 p.m.”

* Redefine the tarmac time limit as of when a plane begins returning to the gate, instead of when passengers are allowed to deplane.

The penultimate point is painfully true. It is cheaper to pay for everyone on the plane to stay in a hotel, than to have to pay the $27,500 fine. (My stay at the Phoenix-Sky-Harbor Embassy Suites was about $70 with the voucher).

When the government effectively prohibits one form of intolerable travel, the airlines shift to a cheaper, even more intolerable form of travel. Incentives matter.