The report does not include recent weather-related flight delays such as the ones that left JetBlue and United Airlines planes idling for hours on taxiways.
"They just don't get it yet," said Dean Headley, an associate professor at Wichita State University who co-authored the study with Brent D. Bowen of the University of Nebraska at Omaha.
One upside, researchers said, was that the overall number of airline complaints has stabilized since hitting a five-year low in 2005.
JetBlue, which rated highest on the list for the past three years, was bumped out of the top slot by Hawaiian Airlines, which made its debut on the list this year. The top three on the 18-airline list were Hawaiian, JetBlue and AirTran, while the bottom three were, from worst to best, Atlantic Southeast, American Eagle and Comair.
Industry spokesman David Castelveter blamed the majority of delays on bad weather. Making matters worse, he said, more planes will be in the air in coming years, and the air traffic control system cannot handle the growth.
"We're going to see more delays and those delays translate to cancellations, mishandled bags and unhappy passengers," said Castelveter, spokesman for the Air Transport Association, a trade group for the major U.S. carriers. "It's not a pretty picture."
Congress needs to provide more money to update the system so it can improve its handling of the increased traffic and weather problems, Castelveter said.
Analysts fault the airlines for trying to cut costs by squeezing more passengers onto fewer planes, CBS News transportation and consumer safety correspondent Nancy Cordes reports.
"I can't remember when I've flown in a plane that had more than two or three empty seats," airline industry analyst Peter Goelz told CBS News. "That's good for the airlines, but when you bump into a problem, there's no margin of error."
The Airline Quality Rating report, compiled annually since 1991, looked at 18 airlines and was based on Transportation Department statistics. The research is sponsored by the Aviation Institute at University of Nebraska at Omaha and Wichita State University.
Among the findings: