Story highlights Congress raised the fee in a budget deal

Most of the money doesn't go to back to the TSA

Increase will be $1.20 or $6.20 for most fliers

The costs of your airline travel will rise a little today, thanks to the federal government.

Airline passenger security fees charged by the Transportation Security Administration are increasing because of the congressional budget deal passed in December.

The September 11 passenger security fee has traditionally been collected to fund the TSA's airport security measures, but not this time. Most of the new revenue will go to pay down the federal deficit.

Until Monday, a passenger was charged $2.50 for each leg of a journey. For a nonstop round trip, the cost was $5. For a round trip with a connection each way, the cost was $10.

The fee was capped at two flights each way. That means you couldn't get charged more than $5 each way or $10 round trip, even if you took three flights to get your destination.

Now, passengers must pay a flat fee of $5.60 in each direction, no matter how many plane transfers are made to get from one city to another.

For passengers flying a nonstop round trip, that means the fee will increase from $5 to $11.20.

Passengers flying round-trip with a connection each way will see their fees increase $1.20 to $11.20 per round trip, versus $10 before the fee increase.

There's one exception: If you book that terrible trip with a long layover, meaning at least four hours when traveling domestically or 12 hours when traveling internationally, the fees start over. Passengers with that much of a stopover between their flights will have to pay another $5.60 for the next leg.

The TSA's interpretation of the fee increase has been called into question. Though the TSA says the congressional budget deal eliminated caps on these fees, top congressional budget writers say that's not true. Sen. Patty Murray, D-Washington, and Rep. Paul Ryan, R-Wisconsin, have written the TSA demanding an explanation.

The trade group Airlines for America has generally objected to government raising more funds from airline passenger travel and specifically objected to this fee increase and the elimination of the fee cap.

"Our government must stop using airlines and their passengers as its own personal ATM whenever it needs more money," according to a statement.

"A4A strongly opposes TSA's elimination of the regulatory regime that rejects congressional intent by removing the cap on the TSA fee increase per enplanement as it will disproportionately harm airline passengers who rely on service to small and rural communities."

Who will pay the fee? Though there's a chance the airlines could absorb some of the cost, don't bet on it.

Southwest Airlines added the fee to its list of taxes and fees charged to customers starting today.

"Effective for bookings starting on July 21, 2014, all domestic air carriers are required to implement an increase in the government-imposed September 11th passenger security fee," Southwest spokesman Nick Blampye wrote in an e-mail.

"The fee increased from $2.50 per segment (with a maximum of $10.00 per round-trip) to $5.60 per one-way trip," Blampye said. "Southwest customers can view a complete fare breakdown at the time of purchase, which includes the current security fee."

Delta Air Lines and United Airlines, which both declined to comment, also appear to be putting the entire cost on passengers. A flight search Monday at Delta.com showed a charge of $11.20 for a nonstop round-trip flight from Atlanta to New York's LaGuardia Airport. So did a United.com search for a nonstop round-trip flight from Atlanta to San Francisco.