The Department of Transportation is no stranger to regulatory backlash, and it very likely anticipated industry complaints when it imposed a series of federal consumer-protection rules on airlines last month.

One of the first complaints to register on the DOT seismograph is from low-fare carrier Spirit Airlines (NASDAQ:SAVE), which added a $2 fee to its tickets to compensate for seats that remain empty after passengers, as allowed under the new rules, cancel their reservations without penalty. As noted in a recent USA Today story, Spirit calls the $2 up-charge the “Department of Transportation unintended consequences” fee.

“People love the idea of not having to commit to a reservation, but this regulation, like most, imposes costs on consumers,” said Spirit’s CEO, Ben Baldanza.

DOT Secretary Ray LaHood isn’t buying that argument. “This is just another example of the disrespect with which too many airlines treat their passengers,” he said. “Rather than coming up with new and unnecessary fees to charge their customers, airlines should focus on providing fair and transparent service — that’s what our common-sense rules are designed to ensure.”

Spirit has led the charge against the DOT’s new regulations, most prominently in its lawsuit aimed at blocking a rule that requires advertised fares to factor in government taxes and fees upfront for consumers. Those charges can boost a $9 Spirit flight–from, say, Atlantic City to Atlanta–to $29, USA Today notes.

As a practical matter, it may be that the tacked-on $2 fee is unlikely to startle many passengers flying Spirit, which keeps fares extremely low but does charge for most extras, including bags that are toted on board.