Transportation Security Administration agents check tickets at a security checkpoint ahead of Thanksgiving Holiday at the Midway International Airport in Chicago, Illinois, 21 November 2014. Photo by Kamil Krzaczynski/EPA

The head of the troubled US Transport Security Administration, Peter Neffenger, has fired its head of security, as the government agency that manages security at US airports faces the worst backlash since it was created in 2001.

The TSA is really, really unpopular at the moment, mostly thanks to the maddeningly long lines at security checkpoints which snake around airports across the country.

It isn't just the public who are exasperated over the glacially slow screening process. Congress is also unhappy with the agency, which was hastily established by the George W. Bush Administration as an arm of the also newly-created Department of Homeland Security just two months after the 9/11 attacks. Since its inception, the TSA has routinely failed undercover tests carried out by DHS, revealing broad flaws within the security apparatus at some of the country's busiest travel hubs.

Last year, undercover investigators were able to smuggle fake bombs, weapons and other contraband through checkpoints in 95 percent of tests.

Kelly Hoggan, who served as head of security since 2013, landed in hot water earlier this month when the House Committee on Oversight found that he had pocketed $90,000 in bonuses during his first year on the job — despite budget cuts, regular security lapses and reported short-staffing.

Despite significant security vulnerabilities, TSA's head of security took home $90,000 in bonuses over 13 months. — Oversight Committee (@GOPoversight)May 12, 2016

"Those bonuses were given to somebody who oversees a part of the operation that was in total failure," Representative Jason Chaffetz, Republican of Utah and the committee's chairman, said.

During his appearance before the committee on May 12, Neffenger announced plans to cap bonuses at $10,000 each year, "halting what I considered an unjustifiable prior practice that replaced no limits on these awards."

Earlier this month, the TSA's chief of operations warned fliers to prepare themselves for worse to come, because hours-long waits were going to get longer, not shorter, during the busiest travel season of the year. "This is going to be a rough summer," said Gary Rasciot. Rasciot said the reason for worsening lines was a combination of a chronic understaffing issue and the need to accommodate changing security threats.

In April, at Charlotte Douglas International Airport, some 600 passengers missed their flights after understaffing led to waits exceeding three hours, an episode which the airport's interim director described as a "fiasco."

According to three former and current TSA employees, the issues driving these long waits go much deeper than budget cuts, changing threats and understaffing. They allege that there's something rotten at the heart of TSA, which is mired in bureaucracy.

Three employees testified to congress in April – including Andrew Rhoades, an assistant federal security director at Minneapolis-St. Paul International Airport – whistleblowing efforts by staff about mismanagement and misconduct often resulted in their forced transfer to other airports, in many cases at the direction of Hoggan.

"As a result of a chilling culture of intimidation and retaliation at the Transport Security Administration," the Oversight Committee wrote in its summary of the April hearings, "security gaps go unaddressed, and senior employees are not being held accountable for misconduct."

"TSA's problems are rooted in the areas of leadership and culture," Rhoades said in his April hearing. "Ours is a culture of misconduct, retaliation, lack of trust, cover-ups and the refusal to hold ... senior leaders accountable for poor judgement and malfeasance. Habitually my agency bypasses merit principles in its allocation of awards and hiring."

"Many senior leaders believe they are untouchable," he added.

According to Rhoades, for example, a "candid and outspoken leader" of theTSA in Florida named Ed Goodwin was reassigned to Des, Moines, Iowa, despite his superiors' full awareness that Goodwin was the primary caregiver for his elderly parents and that his daughter was in high school.

"When faced with the dilemma of choosing between leaving his family or keeping his job, he resigned," Rhoades told Congress. "It's the TSA version of "Game of Thrones."

Rhoades also testified that "not only does the TSA mistreat its employees, it alienates entire communities. On April 8, 2016, my supervisors asked me [to] profile Somali imams and other Somali community members."

However, Rhoades thinks that the decision to replace Hoggan and beef up the numbers of TSA officials in Chicago to improve particularly horrible wait-times at the O'Hare airport aren't enough to make any real change. "The timing of this decision is too late to make a real difference for the summer," Rhoades told the New York Times. "Neffenger is only doing this because the media and Congress are making him look bad."

Mark Livingston, program manager in the agency's Office of the Chief Risk Officer, also testified in April — and claims he was demoted after reporting his superiors for misconduct.

"I am concerned that TSA employees... fear their supervisors more than they fear a potential terrorist threat," Livingston said. "No employee will adhere to the DHS public policy of "See Something – Say Something" when the danger is greater from within the organization than it is from the outside."

Livingston told the Times that "no one thinks [Neffenger] is really making any meaningful changes."

"Bottom line is no one in TSA believes in Neffenger now. He is only acting out of desperation," he said.

Meanwhile, some airports have started taking matters into their own hands, amid consistent failures by the TSA to solve the problem of long waits and understaffing. Officials with the Seattle-Tacoma International Airport announced earlier this month plans to hire 90 full-time, temporary private contractors to streamline security checks this summer.