Let's follow the trail here:

• Colin Kaepernick, and other players who similarly protest are SOBs and disrespect the flag by kneeling;
• Colin Kaepernick and other players who similarly protest state that they are doing so to raise awareness to the clear and distinct disparate treatment that can occur with respect to certain police actions based upon one's race/national origin (backed up by statistical data);
• Critics refuse to accept the players' arguments that they are "standing up" for equality by taking a knee, and adamantly declare that their behaivor is disrespectful to the flag and no other conclusion can  be reached.  

So long story short, a critic of the players who are protesting reacts to their form of protest in a certain way, draws a conclusion with respect to their form of protest, and dismisses their reasons for their protest, regardless of how well articulated or founded.

Flip the script:

• Critic of the protest says I am not a racist, I just refuse to acknowledge the merit behind the protests;
• Critic of the critic says dismissing the players' desire to draw attention to racial inequality is in many ways enabling that racial inequality to continue, and theoretically could be construed as endorsing it;
• Critic says, "I am not a racist" 

So on one hand, we're to accept the statement of "I am not a racist" as fact, even if the person saying it flatly dismisses the opinion of the protestors.  It is logically inconsistent, and founded solely in the result someone wants.  I feel very comfortable in my position that there are many players protesting with legitimate and deeply held convictions who are not at all disrespectful to the flag or what it stands for.  Indeed, they are arguably even more respectful of what the flag stands for than those who stand because they have to, and not because they understand or care why they are.  Of course there are others who are kneelilng, just to go along with the crowd, and likely do not deeply hold the same convictions as Colin Kaepernick and others.  To that same end, I am sure there are people who are legitimately offended who are not dismissive of the viewpoints of the players, but nonetheless feel as though ther are other ways their message could be delivered.  Then there are those who are indeed racist.

The problem when we deal in absolutes, is that it results in absolute nonsense.  Despite what you might want to believe, it is indeed just as reasonable to conclude that someone who is opposed to the protests is racist, as it is to conclude that those that are protesting are unpatriotic.  That is the point here.  It is hypocritical to argue one group is definitely one thing, but not at all reasonable that the other group is the other thing.    

"...and dismisses their reasons for their protest..."

Disagreement with the manner of protest is not a dismissal of or disagreement with the reasons for the protest, despite your labored and lengthy attempt to make it seem logical.