What the American flag means to different people should be self-defined. Some people see the American flag as a representation of their veteran family members, of the countries and values that they respect, and of the country they believe has protected them. But just as everyone feels different emotions after hearing the national anthem play, everyone can have different responses to the pre-game ceremony.
Even Drew Brees, the original footballer who made the comments about the irony of using liberty to complain about a lack of liberty, apologized and realized how insensitive his comments were.
In a country where a black person walking down a street is three times more likely to be killed by police than a white person, and where 98.3% of killings by police from 2013-2020 have resulted in the officer not being charged for the crime, it is completely fair for Kaepernick and others to see police violence as the most important issue in America that must be protested.
How one interacts with the symbols of a country is their own choice, and Kaepernick had every right to not see his country as one that he respected.