Literal flag-worship is an artifact of the religion called Americanism. Stuff like the flag and the anthem are holy symbols of righteousness. What's going on is a reminder that a whole lot of people in the US don't fundamentally conceive of the country in the terms laid out in the constitution. They don't really grasp, much less support, the truer ideals the country is built on.
Like sunday morning Culture Christians, they've been conditioned to think of themselves as part of a rather specific way of thinking, speaking, and doing things for no other reason than it is the way things are done. The right way, and all others are a not just wrong - other ways are a threat to rightness.
And the outsized reactions to "taking the knee" come in part from the fact that as a religion, Americanism isn't a particularly gentle one. It traditionally celebrates the closed fist and the angry, vengeful father. An image of America as a pinnacle of power, that rewards the loyal and pure with victory in all things. One must understand that those kneeling aren't merely ignoring the flag, to believers in Americanism. To kneel or make it visibly known you are refusing to participate in the ceremony, one is actively refuting the primacy of Americanism itself and thus, part of the identity of believers.
It is particularly triggering to people with racist conditioning because, well, you know, it is taken for granted by racists that American supremacy equals white supremacy as well.