Division. For every action, there's an equal and opposite reaction. The knee causes divisions, boos in response cause division, everyone gets more divided.
That's why taking the knee fails. If you're fighting something that should be so obviously universally abhorrent as racism and the mechanism you use to highlight it is being booed, then obviously it's because of one of two things - either there's an incredible amount of racists, around 40% of football fans, who rabidly hate the idea of equal rights, or the gesture has too many other connotations that muddy the waters.
I'd like to think most people, looking at the situation objectively, would come to the conclusion that the latter of those two reasons is much more likely than the former.