Some interpreted the chants as questioning Kaepernick's patriotism for his protest of racial inequality and oppression in the United States. It was an implication Kaepernick vehemently disagreed with after San Francisco's 45-16 loss.
"I don't understand what's un-American about fighting for liberty and justice for everybody, for the equality this country says it stands for," Kaepernick said. "To me, I see it as very patriotic and American to uphold the United States to the standards that it says it lives by."
In continuing his protest, Kaepernick on Sunday knelt during the anthem for the first time as a starting quarterback before a regular-season game. He was again joined by safety Eric Reid and linebacker Eli Harold in supporting the cause.
Safeties Antoine Bethea and Jaquiski Tartt, cornerbacks Keith Reaser and Rashard Robinson, and running back Mike Davis continued their tradition of raising their right fists during "The Star-Spangled Banner."
As Kaepernick, who made his first start since Week 8 of last season, led the offense onto the field, he was greeted by a loud chorus of boos from Bills fans. Those boos continued for the first couple of snaps before dissipating into cheers of encouragement for Buffalo's defense.
During the game, a fan at the stadium tweeted that someone had thrown a bottle at Kaepernick, but if it happened, Kaepernick didn't notice.
"If they did, they didn't have very good aim," Kaepernick said. "But I had some Bills fans before the game come up and say they are supporting me, so I think it all depends on who the person is. At the end of the day, I'm going to continue to fight for what I'm fighting for."
Meanwhile, just off the stadium property, TheMMQB.com reported that outside vendors were selling anti-Kaepernick shirts, including one depicting Kaepernick in the crosshairs of a rifle scope with the words "Wanted: Notorious Disgrace to America."
Last month, Kaepernick said he had received death threats over his protest, but he said Sunday those aren't as frequent anymore.
"Those are rare occurrences now," Kaepernick said. "I think for the most part people are realizing the impact and what's going on, and like I said from the beginning, I knew the consequences of what could come with this, and I was prepared for that."
The fan reaction wasn't all negative, however. A group of Bills fans participated in a "kneel in" outside the stadium to support Kaepernick and his cause.
"That's huge," Kaepernick said. "I think it's something that, once again, people are realizing that these are real issues that affect many people. It's something that has to be addressed. Until us as people recognize and address that some of us have privilege, some of us don't, and some of us are able to do certain things without consequences and others of us can't. Those are all things that need to be addressed.
"Me as a black man that plays football and is considered a celebrity, I'm treated differently than a black man that's working 9 to 5 in the 'hood. That's just the reality of it. It shouldn't be that I'm treated differently than that person or he's treated differently than me. We're human beings, and it should be something that everybody is treated that way."
At the end of the game, Kaepernick exchanged jerseys with Bills wide receiver Marquise Goodwin before changing back into his Muhammad Ali T-shirt. Kaepernick said he wanted to "pay homage" to Ali on Sunday.
"He was someone that he fought a very similar fight and was trying to do what's right for the people," Kaepernick said. "And for me to be able to have someone like that come before me is huge. He is someone that helped pave the way for this to happen with what he did and what he stood for. People remember him more for that than they do as a boxer, and I can't let him die in vain. I have to be able to try to carry that on and try to fight that same fight until we accomplish our goal."
Kaepernick finished 13-of-29 for 187 yards and one touchdown; he also rushed for 66 yards on eight carries. When coach Chip Kelly was asked after the game whether Kaepernick would remain the 49ers' starting quarterback, Kelly said, "Yeah, we'll see," and complimented Kaepernick's play.
"I thought physically he looked good," Kelly said. "I thought he did some good things out there. Again, for his first time back, I thought he did an OK job. We have to be better overall on offense. It's not just the quarterback. It's everybody on the offensive side of the ball."
Kaepernick responds to implications of USA chants in Buffalo
After being asked about fans in Buffalo chanting "USA, USA," 49ers quarterback Colin Kaepernick, who again knelt during the national anthem Sunday, says he doesn't "understand what's un-American about fighting for liberty and justice for everybody."