I can easily buy that the militias started out as being a good thing. Initially I assumed that Monroe and company were like a bunch of redneck "hate the government" militias that became popular back in the 90s and then became the Tea Party. But it seems that Monroe and Uncle Whatshisname seemed to have started off with a simple premise: the blackout destroyed the government, let's rebuild it. At some point they went off the rails. I don't think the show needs to show that the militia is a bad idea, just that Monroe's militia is a bad idea. It could be as simple as Monroe never bothering to create any sort of civilian government but anointing himself as ruler and crushing anyone who questioned him. It could also be more complex: Monroe believes he is a good man, he doesn't want to be killing people or taxing them to death, but at some point he gradually became more and more corrupt to the point where he is the problem but doesn't know it.
Or he could just be a loser who decided to get back at society for being mean to him. In Dies the Fire, the leader of the bad guys was a history professor who recruited his buddies from the Renaissance Fair and a biker gang and restored ordered. Only he totally lost the plot by driving extra mouths into exile and marching into battle under the Eye of Sauron.