(Reuters) - San Francisco 49er Colin Kaepernick was lustily booed by many Buffalo fans on Sunday as he continued his national anthem protest before turning in an inauspicious performance against the Bills.

Kaepernick arrived at New Era Field in Orchard Park, New York paying "homage" to Muhammad Ali by wearing a T-shirt with a picture of the boxing legend and leading civil rights campaigner who died in June.

As he has done all season, the quarterback kneeled during the United States national anthem, along with two team mates, as a police officer stood immediately behind the trio.

Several other San Francisco players raised their right fists in another form of protest.

Before the anthem, sections of the crowd began chanting "USA, USA."

But Kaepernick took issue afterwards at any implication that his stance was unpatriotic.

"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 told reporters after being jeered before the game and out on field.

"To me, I see it as very patriotic and American to uphold the United States to the standards that it says it lives by."

Kaepernick has polarised opinion amongst National Football League fans since pre-season for the silent protest he says is against social injustice and police brutality.

After five weeks on the bench, he was called up to start for the struggling 49ers against the Bills.

In the second quarter he threw a first touchdown pass in 364 days when he found wide receiver Torrey Smith, connecting with a pass for a 53-yard catch-and-run touchdown.

But highlights were otherwise few and far between in a game when he connected with 13-of-29 passes, for 187 yards, as the Bills whipped the 49ers 45-16.

Local media reported anti-Kaepernick T-shirts and other items were being sold outside the stadium.

Video posted on social media showed a variety of anti-Kaepernick sentiment, though there also were signs of support.

"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," he said.

"At the end of the day, I'm going to continue to fight for what I'm fighting for."

He said he was unfazed by the hostility of parts of the crowd.

"To be honest, I was focused on football so I wasn't really listening to what was going on in the stands."

(Reporting by Andrew Both in Cary, North Carolina; editing by Ken Ferris and Ian Ransom)