Houston Texans players have staged a protest against their team’s owner, Bob McNair, after he said “we can’t have the inmates running the prison” when speaking about the NFL protest movement.

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Players have been kneeling before and during the national anthem this season as a protest against racial injustice in the United States. About 40 of the Texans, a majority of the team, did so on Sunday before their game against the Seattle Seahawks, apparently in response to McNair. Some of their team-mates chose to stand. A number of Seahawks players also knelt, as they have done throughout the season.

“I’m never going to force anybody to do anything that they don’t feel comfortable with. I think we all felt the same way on Friday [after McNair’s comments],” Texans guard Duane Brown said after the game. “And as far as the demonstration went, some people didn’t feel quite comfortable doing it, some people did. But we all supported each other, and that was what was important. I don’t think anyone looks at anyone differently for what they stood for or didn’t stand for.”

ESPN reported that McNair’s comments at a meeting last week between owners, team executives and the NFL commissioner, Roger Goodell, “stunned some in the room”.

“After the owners finished, Troy Vincent [NFL executive vice-president of football operations] stood up,” the article said. “He was offended by McNair’s characterization of the players as ‘inmates’. Vincent said that in all his years of playing in the NFL – during which, he said, he had been called every name in the book, including the N-word – he never felt like an ‘inmate’.”

McNair reportedly apologized to Vincent later, “saying that he felt horrible and that his words weren’t meant to be taken literally”.

In an official statement, McNair said: “I regret that I used that expression. I never meant to offend anyone and I was not referring to our players. I used a figure of speech that was never intended to be taken literally. I would never characterize our players or our league that way and I apologize to anyone who was offended by it.”

On Friday, the Texans wide receiver DeAndre Hopkins was an unexpected no-show at practice. The head coach, Bill O’Brien, declined to address whether it was related to McNair’s controversial comments.

McNair, an energy and real estate magnate who is estimated to be worth $3.5bn, backed Donald Trump for president – giving a Super Pac $2m in 2016 – and then donated $1m to Trump’s inauguration committee. The US president is a vocal critic of the NFL protest movement.

“Wouldn’t you love to see one of these NFL owners, when somebody disrespects our flag, to say, ‘Get that son of a bitch off the field right now. Out! He’s fired. He’s fired!’” Trump said in September.

The protest movement is becoming an increasing worry for NFL owners, some of whom believe it is hitting the league’s bottom line. The league’s television ratings are down this season, although it is not clear whether this is directly linked to the protests, as TV sports audiences have fallen across America. The Dallas Cowboys owner, Jerry Jones, has said he would bench any player who knelt during the anthem and has said sponsors have told him they are worried about the protests putting off customers. “There is no question the league is suffering negative effects from these protests,” Jones said last week.