The report ranked the 14 largest U.S. airlines on input from more than 16,000 travelers. The criteria included consumer complaints like mishandled bags and being turned away for over-booked flights. It also included on-time and late arrivals.
Southwest Airlines ranked second on the list, followed by JetBlue. Both airlines charge relatively few fees. At No. 4 came Hawaiian Airlines, then Alaska Airlines at No. 5.
Fees for checked baggage and limited leg room are among the many gripes expressed in the survey.
"A full third of survey respondents complained about crowded flights and a quarter complained about cramped seats," said Karen Jaffe of Consumer Reports.
No-frills Spirit Airlines hit rock bottom on all of the customer benchmarks, including seating comfort, cabin staff service, cleanliness and baggage handling.
United Airlines, U.S. Airways and American Airlines did slightly better overall, but like Spirit, they got low scores for cleanliness and leg room.
"There are airlines out there where you can have a more comfortable flying experience. They just may not fly everywhere you'd like to go," Jaffe said.
At the bottom of the rankings were Spirit, United, American, U.S. Airways and Delta Air Lines.
Some airlines have responded to passengers' frustration over fees by "bundling" services together - for a fee. A bundle might include preferred seating, free checked baggage and free flight changes. But Consumer Reports says passengers should make sure to use all the benefits, otherwise paying à la carte fees might be cheaper.
The Associated Press contributed to this report.