Obama made his comment during a news conference Monday in Hangzhou, China, where he is attending a meeting of Group of 20 countries.
Kaepernick has said he is refusing to stand during the national anthem to bring attention to what he considers failings in the United States' treatment of racial minorities.
The president said he hasn't paid close attention to Kaepernick's protest, but he added that he has no doubt that Kaepernick is sincere and "cares about some real, legitimate issues that have to be talked about."
"There are a lot of ways you can do it," Obama said of speaking out. "As a general matter, when it comes to the flag and the national anthem and the meaning that that holds for our men and women in uniform and those who fought for us -- that is a tough thing for them to get past to then hear what his deeper concerns are."
Kaepernick kneeled during the national anthem during the 49ers' final preseason game last week. He had sat during the anthem in previous preseason games.
Women's soccer player Megan Rapinoe kneeled during the anthem before an NWSL game Sunday, calling it "a nod to Kaepernick."
The 49ers have named Kaepernick as the team's backup quarterback behind Blaine Gabbert. Kaepernick's protest did not play a factor in the decision to keep him on the roster or make him No. 2 on the depth chart, coach Chip Kelly said Saturday.
Information from ESPN staff writer Nick Wagoner and The Associated Press contributed to this report.