Speaking in China, Mr Obama said the player had raised legitimate issues.
Mr Kaepernick stirred controversy when he sat during the national anthem to protest against racial injustice.
Some players have followed his example and sat or kneeled through the anthem.
Asked about the issue during a news conference at the G20 in Hangzhou, President Obama said it was tough for those in the military to understand why Mr Kaepernick might snub the national anthem.
But he said he did not doubt his sincerity to raise issues.
"If nothing else, what he's done is he's generated more conversation around some topics that need to be talked about," the president said.
He added he would rather have young people engaged in the argument in a democratic process than "people who are just sitting on the sidelines and not paying attention at all".
A week after staying seated during The Star-Spangled Banner, the San Francisco 49ers quarterback kneeled during the anthem before a match on Thursday.
Team-mate Eric Reid also kneeled, but they were booed by some in the crowd.
On Sunday night, US women's soccer star Megan Rapinoe knelt during the national anthem before the Seattle Reign's game against the Chicago Red Stars in what she said was "a little nod"' to Mr Kaepernick.
Mr Kaepernick has said he will continue to sit out the national anthem until he sees improvements in US race relations.
A string of recent police killings and subsequent revenge killings have sparked protests across the nation.
US President Barack Obama has said NFL quarterback Colin Kaepernick, who refused to stand for the US national anthem, was exercising his constitutional right to make a point.