It's actually not that simple. When you've been brought up to react a certain way to your country and it's flag, you can't suddenly tell someone that he's suddenly in the wrong for continuing to do what he's always done (in this case stand). Everyone has different life experiences and perspectives, and if you look closely enough at ANY country, you'll find huge warts which tell you that you probably shouldn't support everything your country has ever done. Should Canadian players not stand for our anthem because of how the Canadian government performed genocide against First Nations people? If Carey Price decided to protest during the anthem, would every other player suddenly have to protest and support that because he did it first and he's in the right?
The fact that people unquestioningly do what they've been told to do from birth without thinking about it is precisely what makes attacking that learned behavior a provocative form of protest. If you're protesting and not being provocative, it means nobody is listening to you.
And the big difference between the hypothetical you've laid out compared to the present protests is that the current protests are tackling a contemporary issue, not a historical one. The things happening to black people in America are happening
right now. Protesting the violence and injustice that is occurring right this very moment is something that could, theoretically, lead to concrete change in both the immediate and long term future. It
could save the lives of black children who exist right now.
By contrast, protesting the historical exploitation and eradication of native peoples might be a noble gesture, but no amount of kneeling is going to restore any of those lost tribes. You can't have a political movement when there's nothing to be gained. This would make such an action more of a tribute or a remembrance, rather than a protest.