Trump on the other hand, called the act of kneeling before the anthem "big progress".
Amid a series of tweets Saturday against criticism of the federal response to hurricane damage in Puerto Rico, the president returned to the world of sports and society: "Very important that NFL players STAND tomorrow, and always, for the playing of our National Anthem".
Several other players protested by kneeling or raising a fist during the anthem during the 2016 season or early in the 2017 season before Trump's remarks prompted a more widespread response from National Football League teams.
The Jets locked arms for the national anthem.
After last week's widespread demonstrations during the national anthem by players, coaches, and owners across the NFL, many teams attempted more generic displays of unity during Week 4. On Tuesday, Trump called on the NFL to ban players from kneeling in protest at games while the national anthem is played.
Almost half of the 49ers' roster were kneeling during the national anthem, while the rest of the team stood behind.
"And there are few things that are more important to me than the honour that I feel we must bestow upon our military men and women - the honour we must show our flag - and standing at attention for our flag and our national anthem is a powerful symbol we must respect".
He added: "Respect our Flag and our Country!" They are about specific social justice issues.
"I think what matters is that we have to show people that we are an inclusive society, that we want everyone to succeed", he said.
The NFL rejected the president's remarks as not factual.
Trump has spent days attacking players who kneel during the anthem. The protests culminated a week ago when scores of players, following calls by the president to fire protesting athletes, sat or knelt as the anthem was played.
And on Thursday he continued the crusade, drawing a rebuke from the NFL after he said football team owners are afraid of their players. "I think everyone has the right to protest, but I think you have to choose your stage wisely", said Laura Williams, who works in healthcare.
Unlike last week when the Pittsburgh Steelers stood in the tunnel during the national anthem, players were on the sideline as the anthem was performed.