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:
The increase in lost bags comes as at least one domestic carrier — Spirit Airlines — plans a new fee for passengers who check their bags. Come June, Spirit will charge $5 each for one or two checked bags if the ticket was booked online and $10 each for passengers who do not book online.
Headley does not think the idea will fly with consumers, who long have expected their ticket prices to include a checked bag or two. "It will set off an absolute atomic bomb," he said.
Baggage problems are due to airlines cutting the number of employees on their ground staffs over the past few years, Headley said at a news conference Monday.
On-time performance, the report said, worsened last year, with 75.5 percent of flights arriving on time, compared with 77.3 percent in 2005.
JetBlue took a hit in February, when passengers on 10 planes spent from 5 to 10 1/2 hours sitting on runways at John F. Kennedy International Airport in New York because of icy weather and gate congestion.
It took days for the airline to recover from the February storm and resume normal operations. That led JetBlue to establish a customer bill of rights promising vouchers to passengers who experience delays.
Some lawmakers want to pass legislation establishing certain rights for air passengers. The airlines oppose the move. "Legislating what is the right thing to do for a service provider usually won't work," Headley said.
Overall, complaints about the airlines last year held steady at about 0.88 complaints for every 100,000 passengers. Nearly half the complaints were about flight problems or baggage.
"It just seems to me that consumer expectations have been lowered," Headley said, explaining that at the end of the 1990s and in 2000 the numbers of complaints were much higher, even though problems with baggage and delays were less frequent.
The study found an increase in the number of passengers bumped or denied boarding because of oversold flights — 1.01 denied boardings per 10,000 passengers last year, compared with 0.89 per 10,000 in 2005. JetBlue had the lowest rate of bumped passengers; Atlantic Southeast the highest.
But also, overall, customer complaints have actually dropped slightly — though the authors of the study say that might just be because customer expectations have dropped, too, Cordes reports.