No modern government (including democracies) are ever comfortable with citizens organizing and arming themselves, no matter what the cause is. Governments fear organized and armed citizens because there is a possibility that they may be tempted to challenge the government. If the Minutemen crosses the line on the law, even a minor infraction, the federal/state LE are instructed to come down hard and cause legal hardships to see if they can discourage recruitment of law abiding citizens. If the Minutemen are well discipline, then the federal/state will infiltrate the organization with provocateurs and start an incident, so the organization will get into more legal problems and become discredited by the MSM. I think right now, the US government is gearing up their covert and legal resources to destroy the Minutemen because they cannot afford an armed paramilitary within the US that may challenge them in the future.
Then I suggest a course correction back to the Constitution as the founders envisioned it.