Trump has been on a three-day crusade since he first commented on the protests at a rally in Alabama Friday
, when he said that coaches should get the "son of a bitch" off the field if the player continued to kneel. His chief of staff, a lifelong Marine who was brought in to introduce order into the West Wing, is attuned to race issues and voiced his concern about the matter, one official said.
In a brief interview Monday evening, Kelly told CNN he is "appalled" by what he sees as a lack of respect for the flag and national anthem.
"I believe every American, when the national anthem is played, should cover their hearts and think about all the men and women who have been maimed and killed," Kelly said. "Every American should stand up and think for three lousy minutes."
His son, Robert Michael Kelly, was killed in combat in Afghanistan in 2010.
Kelly declined to talk about the President's decision to wade into the issue. White House officials say they believe this will blow over, but did not know how long the President would keep it alive.
Two distinct issues are driving the national debate: Believing players should stand during National Anthem and the question of whether it's wise for a president to make issue of it.
After the story appeared on CNN, the President criticized the network, calling it "fake news."
"@CNN is #FakeNews. Just reported COS (John Kelly) was opposed to my stance on NFL players disrespecting FLAG, ANTHEM, COUNTRY. Total lie!" the President wrote
"General John Kelly totally agrees w/ my stance on NFL players and the fact that they should not be disrespecting our FLAG or GREAT COUNTRY!" he said in a second tweet
Kelly attended the Alabama rally and Trump brought him on stage for praise just minutes before he made his NFL comments. Kelly was unaware Trump was going to wade into a culture war just moments later, an official said. The comments were not included in his prepared remarks.
Though they drew immediate criticism, Trump has not relented. The next day he called for NFL fans to boycott games unless the league fired or suspended players who refuse to stand for the national anthem, and has tweeted more than a dozen times about the matter.
Two sources close to Trump -- one inside the White House and one outside -- said they have never heard the President complain this vociferously about the NFL protests before. But Trump has previously singled out former San Francisco 49er quarterback Colin Kaepernick, who drew national attention last year for protesting police brutality, especially aimed at African-Americans, by refusing to stand during "The Star-Spangled Banner" prior to kickoff.
"It was reported that NFL owners don't want to pick him up because they don't want to get a nasty tweet from Donald Trump," he said during a campaign-like rally in Louisville, Kentucky. "Do you believe that? I just saw that. I just saw that."
Yet Trump has typically only spoken in glowing terms of his relationships with people in the league, such as New England Patriots Chairman and CEO Robert Kraft and quarterback Tom Brady.
Both Kraft and Brady have distanced themselves from Trump's remarks.
"I certainly disagree with what he said," Brady said during an interview on sports radio Monday. "I thought it was just divisive."
"I am deeply disappointed by the tone of the comments made by the President on Friday," Kraft said. "I am proud to be associated with so many players who make such tremendous contributions in positively impacting our communities."
Though Kelly has sought to instill discipline in a chaotic White House, it's becoming clear there are two things he can't control: what the President says off-the-cuff and what he tweets. The question now is whether Kelly can now persuade Trump to move on from his battle with the NFL, but one official said he shouldn't count on it.
Kelly was also frustrated with the President
after he said there was "blame on both sides" of the deadly clashes in Charlottesville. He was part of a group of senior advisers who had convinced the President days earlier to more forcefully declare that neo-Nazis and KKK members were "repugnant" after he had condemned them in muted terms at first.
Trump, who often veers off-script when he is surrounded by supporters at his rallies, later said the words "were perfect."
White House press secretary Sarah Sanders defended the President's comments from the briefing room podium Monday, saying that they were not intended to be divisive.
"This isn't about the President being against anyone," Sanders said. "This is about the President and millions of American being for something" -- like "honoring our flag."
"We certainly respect the rights that people have," Sanders said. "This is about the President being for respect in our country, through symbols like the American flag, like the national anthem."
But his remarks struck many as stoking racial resentments because the players he criticized were black and their protests were meant to highlight racial injustice. Trump, however, told reporters Sunday his objections had nothing to do with race.