The poll of more than 2,000 Americans by the travel website TripAdvisor.com also showed that despite the annoyances, more Americans plan to fly domestically and internationally this year compared with 2012.
"Flyers continue to voice concerns about the challenges associated with air travel, such as extra fees and limited legroom," Bryan Saltzburg, general manager of TripAdvisor Flights, said in a statement.
"However, it seems equally clear that these challenges are not limiting the increasing demand for flights."
Travelers complained about fees airlines assess for checked baggage and carry-on baggage, seat selection, printed boarding passes at the airport and in-flight amenities.
Although 38 percent of travelers listed the lack of legroom as their main complaint, they were reluctant to pay a premium for it.
Eighty-five percent of respondents said they would pay less than $25 for a seat upgrade, but 44 percent said they had never paid extra for a better seat. On international trips, most people said they would be willing to pay $50 or less for an upgrade.
Travelers were also looking for savings in other areas. More than 80 percent of those surveyed said they would forego in-flight entertainment for a significantly cheaper flight, while 63 percent said they were unwilling to pay extra to sit in a designated quiet section.
Frequent flyer programs were popular, with 87 percent saying they had participated in one. Smaller numbers had exchanged points for a free or discounted fight or for seat upgrades.
Internet access during a flight was a determining factor with a quarter of people polled saying they would choose one airline over another if it offered access while 37 percent considered their iPad or other tablet device an essential carry-on.