He is refusing to stand for the The Star-Spangled Banner in protest against the plight of black people in the US.
On Sunday Kaepernick, 28, threw his first touchdown pass in 364 days in the 49ers' 45-16 loss to the Bills.
"To be honest, I was focused on football," Kaepernick said.
"I really wasn't listening to what was going on in the stand," he added.
Some fans also chanted "U-S-A" before the national anthem at Buffalo's New Era Field, while t-shirts featuring the player's face and a rifle target were reportedly on sale close to the ground.
Kaepernick added: "I had some Bills fans come up before the game and say they support me."
The quarterback said he has received death threats as he continues his protest, which stems from racial tensions that increased across the nation this year amid a string of police killings and subsequent revenge attacks.
His protest has drawn strong reactions both in opposition and support, with some fans calling it disrespectful to the US flag.
But some veterans and military members have tweeted their support for Kaepernick with the hashtag #VeteransForKaepernick.
"At the end of the day, I'm going to continue to fight for what I'm fighting for," he said. "I think the message carries weight because people realise what's happening - it's something that needs to be addressed."
Asked about a claim that someone in the stands threw a bottle at him, Kaepernick replied: "If they did, they didn't have very good aim."
San Francisco 49ers quarterback Colin Kaepernick, who has polarised opinion by kneeling during the national anthem, was booed on his return to the starting line-up against the Buffalo Bills.