You are mistaking the machinery of power for the reality of power.
In the final analysis, power does indeed grow out of the barrel of a gun, precisely why the Founders added the Second.
Every person in our Armed Forces takes an oath not to the government or the president, but to the Constitution.
Given the strong military culture of honor, I suspect any attempt by politicians to bypass the constitution would result in armed resistance by the military, more or less what happened in Chile under Pinochet.
For a political coup to succeed, the government would have to first gain operational control over the military. This would require replacing huge numbers of officers and would require at least a decade, probably longer, and could not be done discreetly.
Could this all happen? Sure, but it would take a very long time and I’m not concerned about it any time soon.
Not to mention many millions of the “unorganized militia.”