Josh Peter

USA TODAY Sports

SAN DIEGO — After hearing loud and sustained boos directed at him during the San Francisco 49ers’ preseason game against the San Diego Chargers on Thursday night, Colin Kaepernick called the crowd’s negative reaction a “misunderstanding.”

Kaepernick, the 49ers quarterback, said the reason he refuses to stand for the national anthem has been distorted. He also said he will donate $1 million to groups that help people affected by the issues he is trying to spotlight — such as racial inequality and police brutality — with his continued protest.

“The media painted this as I’m anti-American, anti-men-and-women of the military and that’s not the case at all,’’ Kaepernick said after playing the first half of the 49ers’ 31-21 victory over the Chargers. “I realize that men and women of the military go out and sacrifice their lives and put themselves in harm’s way for my freedom of speech and my freedoms in this country and my freedom to take a seat or take a knee so I have the utmost respect for them.

“I think what I did was taken out of context and spun a different way.’’

Without providing specifics, Kaepernick said he is working with organizations in communities of need that will get the $1 million he makes this year.

“I’ve been very blessed to be in this position and to be able to make the kind of money that I do and I have to help these people,’’ said Kaepernick, whose $11.9 million salary this year has already been guaranteed. “I have to help these communities. It’s not right that they’re not put in the position to succeed or given those opportunities to success.’’

If the game Thursday night is any indication, not everybody will be cheering for Kaepernick regardless of his $1 million pledge or efforts to clarify any misunderstanding.

During the singing of God Bless America he remained standing and applauded. (“Once again, I’m not anti-American,’’ he later told reporters. “I love America.”)

Then Kaepernick, who sat in protest during the anthem Aug. 26 before the 49ers' game against the Green Bay Packers, kneeled before the national anthem.

Seahawks' Jeremy Lane joins Colin Kaepernick's protest, sits during national anthem

He said kneeling rather than sitting was a gesture of respect for servicemen during the Chargers’ 28th annual Salute to the Military game. Nonetheless, many in the crowd of 47,407 booed as the quarterback dropped to a knee on the 49ers' sideline.

After the game, while approaching a tunnel that leads to the visitor’s locker room, he suddenly cut to his right and jogged toward dozens of 49ers fans to chants of "Kaep! Kaep! Kaep!"

As he signed autographs and posed for pictures, it was clear the fans' affection was not solely a product of his solid performance on the field — 11-of-18 passing for 103 yards and 38 yards rushing on four carries. Many urged him to continue to stand up for his beliefs and others yelled, “Kaep for President!”

Abdisahman Bool of San Diego squeezed his way to the front of the pack, close enough to tell Kaepernick, “You’re the voice for all of us.’’

Yet moments later, as a 49ers team official pulled Kaepernick away from the fans and into the tunnel, a man snidely insinuated Thursday night’s game would be Kaepernick’s last. He suggested the 49ers will cut Kaepernick and free up the quarterback to focus all his attention on drawing attention to himself.

Kaepernick frowned.

“It’s not for me,’’ he said before ducking into the tunnel and heading to the locker room.

Later, Kaepernick said the encouragement he heard was especially meaningful because of the people from which it came. Many of the fans were of color, just like the biracial 49ers quarterback who led them to Super Bowl XLVII in the 2012 season.

“More than anything, the people just saying, ‘We support you, we’re with you, don’t let anybody deter you from what you’re trying to do,’ " he said. “And I think that sticks with me because a lot of those people are people that I want to give equal opportunities to.’’

Toward that end, Kaepernick said he plans to keep kneeling during the national anthem, but also suggested that at some point his protest could end.

“I want to be able to affect change,’’ he said, talking about how people, groups and communities can impact the changes he seeks. “I think when that happens, I think a lot of people will really influence me to stand.’’

PHOTOS: Kaepernick's protest