The San Francisco 49ers quarterback started the protest last month after he sat
during the national anthem for a preseason game, saying he would not "show pride in a flag for a country that oppresses black people and people of color."
Since then, other professional athletes have also chosen not to stand for the national anthem, sparking a national debate.
A member of the audience at the town hall, which was moderated by CNN's Jake Tapper, asked what the President thought about Kaepernick's protest.
"Lately, some players in the NFL have been choosing to take a knee during the national anthem, a time which I believe should be reserved to respect our service members," the man said. "As commander in chief, how do you feel about those NFL players choosing this respected time to voice their opinions?"
Obama responded: "Well, as I've said before, I believe that us honoring our flag and our anthem is part of what binds us together as a nation. But I also always try to remind folks that part of what makes this country special is that we respect people's rights to have a different opinion."
Obama added that he believes protesters should be aware that the reason they are able to share their opinions are because people "fight" for them to be able to do so.
"The test of our fidelity to our Constitution, to freedom of speech, to our Bill of Rights, is not when it's easy, but when it's hard," he said. "We fight sometimes so that people can do things that we disagree with ... As long as they're doing it within the law, then we can voice our opinion objecting to it but it's also their right."
The President also continued that it is important for "everybody to listen to each other."
"I want (the protesters) to listen to the pain that that may cause somebody who, for example, had a spouse or a child who was killed in combat and why it hurts them to see somebody not standing," Obama said. "But I also want people to think about the pain he may be expressing about somebody who's lost a loved one that they think was unfairly shot."
Earlier this month, Obama made similar comments about the quarterback, saying he was "exercising his constitutional right" by not standing for the national anthem.
"I got to confess that I haven't been thinking about football while I've been over here and I haven't been follow this closely," Obama said September 5 during a news conference at the conclusion of the G20 summit in China
. "But my understanding, at least, is that is he's exercising his constitutional right to make a statement. I think there's a long history of sports figures doing so."