I am not missing anything. To you, in this case, silent kneeling is more offensive than vocal booing because you find the kneeling disrespects the anthem and the flag more.
If you really wanted to get to the root of the problem, you'd find that they are kneeling because they believe the ideals America is supposed to represent are not being lived up to.
Here's Eric Reid explaining the reason he started kneeling with Kaepernick:
https://www.nytimes.com/2017/09/25/o...-protests.html
If you want to really get to the root of the problem, you'd might logically find that their kneeling, from their perspective, is patriotic because it puts the idea of freedom and justice for all (the last words of the American pledge of the allegiance), the actual practice of that ideal, over the mere symbol of the nation.
Because what is the worth of a nation when its symbols mean more than the practice of its ideals?