Here are four likely theories.
1. Trump likes him
From choosing a White House physician to lead Veterans Affairs, to plucking TV personalities to fill key spots in his administration, to shuffling his CIA director into the secretary of state spot, Trump has repeatedly placed his own personal views of someone over their qualifications and what the rest of Washington thinks.
That appears to be playing a role in Trump's quiet defense of Pruitt. Pruitt is far from the only socially conservative, climate-change skeptic out there Trump could find to lead the EPA. But Trump likes him, likes that his base likes Pruitt, and likes what he has done for him, by leading the deregulations of Obama-era protections Trump can brag about with his base.
Just look at how a West Virginia congressman praised Pruitt in a congressional hearing. Rep. David B. McKinley (R) said the EPA's rollback of regulations on the fossil fuel economy has given his state “hope.”
“There is some hope we are seeing the economy start to rebound, thanks to you and the administration taking this fight on,” McKinley said.
Trump, ever mindful of how what he does in Washington will be perceived in the states that voted for him — like West Virginia — may have calculated that keeping a damaged Pruitt is more popular with his supporters than kicking him to the curb.
2. Backing down is anathema to Trump
Trump has a reflex to defend people in his orbit who have been accused of behaving badly.
An aide accused of physically abusing two of his wives. A Senate candidate accused of initiating sexual contact with teenage girls when he was in his 30s. A former adviser who pleaded guilty to lying to the FBI. A doctor accused by 23 current and former colleagues of drinking on the job, fostering a hostile work environment, handing out pills like candy and crashing a government car while drunk. These are all people Trump has defended when most of the rest of Washington has abandoned them.
Add to that an aide who brushed off Sen. John McCain's (R-Ariz.) concerns about a CIA nominee because he was “dying anyway.”
Trump is so loyal to certain people it has even brought him legal scrutiny. Special counsel Robert S. Mueller III is looking into Trump's alleged request to the FBI that they back off his fired national security aide, Michael T. Flynn, whom Trump allegedly defended as a “good guy” after he fired him.
3. It might be too late now to fire Pruitt
Pruitt's ethical troubles are not new. He made headlines in March for his $50-a-night rental agreement for a condo in D.C. that is linked to a fossil fuel lobbyist.
Then there were raises he gave two top aides, over White House objections. A soundproof $43,000 phone booth in his office. Flying first class on the taxpayer's dime. His shaky defense of all this in an April congressional hearing.
The White House has stopped saying nice things about Pruitt and tacitly acknowledged his job performance struggles by saying they are looking into all this. To kick Pruitt out now might make it look as if they are caving to public pressure after months of trying to hold strong.
The White House consistently prioritizes saving face. Case in point is another troubled member of the Trump administration, White House aide Kelly Sadler. As of Tuesday she longer works in the White House after weeks of questions about why the White House has not apologized for her comment that McCain is “dying anyway.” (Sadler privately apologized to the McCain family.)
From the outside looking in, it appeared the White House had finally acknowledged its defense of Sadler was not working.
Hours after she was fired or forced to resign, Trump adviser Kellyanne Conway was on TV saying Sadler could have a job elsewhere in the Trump administration. Another official told The Post's Josh Dawsey she was not leaving over her McCain comments but, rather, an internal dispute over the fallout from it.
4. Republicans have not been making a big stink about Pruitt
Trump is facing lots of pressure from Republicans on lots of different fronts. But not really when it comes to Pruitt's job security.
For the most part, an embattled Pruitt got a welcome reception from the right when he went to Congress in April. Sen. Rand Paul (R-Ky.) has called him “brave;” House Republican lawmakers tossed him softball questions in a contentious hours-long hearing.
Two Iowa senators have said Pruitt needs to go; Sen. Joni Ernst (R-Iowa) said he is “about as swampy as you get here in Washington, D.C.” But she and Sen. Charles E. Grassley (R-Iowa) were not responding to the Chick-fil-A news. Their beef with Pruitt is over a wonky policy proposal about gasoline and diesel, reports The Post's Dino Grandoni.
So if Trump wants to keep Pruitt around, he will not hear much grumbling from Republicans.