(CNN) โ€” Even if youโ€™re flying commercial for the holidays, private jets might be making your trip more expensive.

Thatโ€™s because, some critics say, business jets and others arenโ€™t paying their fair share for the nationโ€™s air traffic control system.

The overwhelming majority of the Aviation Trust Fund โ€” the main source of funding for the Federal Aviation Administration โ€” comes from a variety of fees levied on commercial passengers; in contrast, business jets pay only a modest fuel tax.

โ€œIf youโ€™re standing in line forย a commercial flight at Thanksgiving, youโ€™re subsidizing private jet travelers,โ€ said Chuck Collins, a senior scholar at the Institute for Policy Studies, a think tank that specializes in inequality and environmental issues. โ€œWe, the commercial plane travelers, are picking up the slack for the most luxurious type of travel.โ€

Those taxes and fees airline customers pay include a 7.5% tax on the cost of every ticket, a $5.20 tax per trip segment, additional taxes on international flights, or flights to or from Alaska and Hawaii โ€“ even a 7.5% tax on the value of frequent flyer miles being awarded.

There are roughly 20,000 business jets based in the United States, according to the National Business Aviation Association (NBAA), the industry trade group. Thatโ€™s more than twice as many commercial passenger aircraft, but because the business jets fly less, they only account for about 9% of daily flights.

The NBAA argues that the fuel tax of 21.8 cents a gallon, paid by private jet operators to the FAA, covers their fair share of the Aviation Trust Fund. Since business jets use more fuel than smaller planes, they pay a bigger share of the aviation fuel tax than small prop planes owned and flown by individuals, although less than the fuel taxes paid by airlines.

โ€œItโ€™s a very efficient tax, and itโ€™s a progressive tax,โ€ said NBAA CEO Ed Bolen.

But critics say that fuel tax only covers a fraction of business jetsโ€™ costs to the US air system.

The fuel tax only covers about 10% of business jetsโ€™ costs to the FAAโ€™s air traffic control activities, said Robert Poole, director of transportation policy at the Reason Foundation, a libertarian think tank. โ€œTheyโ€™re getting a very generous free ride,โ€ he said.

Non-commercial jets paid $166 million in fuel tax last year, compared to $11.9 billion commercial airline passengers paid in fees and taxes, FAA data shows.

Business jets have other advantages, too. Starting November 7ย during the government shutdown, the FAA ordered commercial airlines to reduce the number of flights by up to 10% at the nationโ€™s 40 largest airports, citing the shortage of air traffic controllers. That left tens of thousands of air passengersย delayed or even strandedย atย large and smallย airports across the country.

But it wasnโ€™t until more than a week later, on November 13, that the FAA limited most business jets flight into and out of the nationโ€™s 12 largest airports.

โ€œYou can sort of see the priorities,โ€ said Collins. โ€œThey should have grounded private planes before you grounded commercial travelers.โ€

Airline passengers wait on November 7, as hundreds of domestic flights were canceled due to a shortage of controllers during the government shutdown. In contrast, private jet flights at major airports did not face restrictions until November 13. Credit: Ronaldo Schemidt/AFP / Getty Images via CNN Newsource

The FAA did not comment on CNNโ€™s questions for this story.

The NBAAโ€™s Bolen said private jets, which are largely used by smaller firms, help businesses contribute to the economy.

Bolen said business jets donโ€™t add much cost to the system because they donโ€™t increase the number of air traffic controllers needed. His groupโ€™s figures show only 3% of the flights at the nationโ€™s busiest airports are by business jets.

โ€œItโ€™s clear traffic systems are built to accommodate the requirements of the commercial airlines, and others fit into that system,โ€ he said, calling air traffic control system costs for business jets โ€œincremental.โ€

When business jet flights were sharply reduced at Reagan National Airport outside of Washington, DC, after the September 11 attack, the airportโ€™s control tower costs โ€œdid not go down one dime,โ€ he said.

But 254 smaller regional airports frequently used by business jets andย private planesย have few, if any, commercial flights

Those airports have their own private controllers, known as โ€œcontract towers,โ€ paid for under contract with the FAA. That system costs about $230 million a year, said Michael McCormick, professor of air traffic management at Embry-Riddle Aeronautical University in Daytona Beach, Florida. And the business jet fuel tax contribution to that system is a small fraction of that cost.

โ€œTheyโ€™re very happy with the status quo,โ€ said McCormick, adding that the business jet owners frequently lobby Congress against changing that.

The Reason Foundationโ€™s Poole says companies would likely pay up to keep their CEOs flying private even if fees were raised significantly. Most of the rest of the world taxes flights based on the gross weight of the plane times the miles flown, Poole said.

โ€œWhenever one of those planes flies outside of US air space, they pay those fees,โ€ he said.