Do you really believe a shotgun will deter the most powerful military machine the world has ever known from doing whatever the fuck it wants to do? Fact is, if they truly wanted to "trample your rights" they would have been trampled already.
Actually, history has proven that no military, no matter how powerful, no matter how brutal, can ever conquer an armed civilian population. It's a lesson the Soviets learned in Afghanistan, one we re-learned in Afghanistan, one everyone learned in Iraq, and one the British learned when their colonies rose up and demanded independence.
Think about it for a moment: the Declaration of Independence was a formal declaration of treason against the Crown, which at the time controlled the most powerful military machine the world had ever known. That open declaration of treason was signed not by a battle-hardened group of freedom fighters with CIA training, but by a group of farmers, doctors, and lawyers. Those same farmers, doctors, and lawyers beat that most powerful military machine in the world multiple times over the course of decades until finally they were left to do as they wished. The Soviets thought that maybe modern technology would make a difference, so they tried carpet bombing the Afghans into oblivion and eventually had to give up and run away. The US thought that maybe more modern technology and better tactics would make a difference, but the Taliban is still there and we're resigned to the fact that they always will be.
You see, so long as a group is willing to fight and die for their cause, and so long as they're sufficiently well armed, it doesn't matter how big and bad your military is. It doesn't matter how many of their fellow citizens they're willing to murder before they decide to turn 'round and shoot in the other direction. So long as people can organize themselves and have the means to exert force, a popular movement is unstoppable. A single guy with a shotgun is no match for a fully equipped military. A fully equipped military is no match for a pissed off populace armed with shotguns, handguns, semi-automatic rifles, and other instruments of war. And the idea isn't to rejoice at the opportunity to live through such a Hellish conflict, but rather to ensure that the government doesn't cross that line into oppression which would trigger such a thing.
I hate to bring it up because I don't think it's a great example of a good David versus a bad Goliath (i.e. the "little guy's" argument and methods leave a lot to be desired in this case), but the Bundy Standoff is most certainly an example of how suddenly government agents who are used to being able to use force to perform their duties get real polite real quick when met with an opposing force of dedicated and armed individuals. That's not to say that the Federal government lacks the resources to do whatever it wants by force at that ranch, but a bloody use of force on American soil has historically created a major backlash among the people (e.g. Waco, Ruby Ridge, etc) and raises the risk that additional incidents like it could spark serious unrest.
Which leaves the government in a challenging position. It can back down and work toward a peaceful resolution that doesn't risk bloodshed, it can tell its agents to use whatever force is necessary to do their job and have huge shootouts broadcast live on CNN, or it can send in Apache gunships to kill everyone who opposes them live on CNN. They (thankfully) elected to go with the least risky option of working everything out peacefully. But can you imagine the social unrest if you'd had CNN broadcasting Federal troops firing on (or slaughtering, as in the crazy overreaction option) American citizens on US soil over a land dispute? There would have been Congressional hearings, investigations, mass resignations, possibly indictments, etc. And if the government didn't do all that and basically told the people to go f themselves, the resulting unrest would be vastly worse.