If they're called "Minuteman", then they're just random NPCs walking around like the cops on foot patrol.
I don't have any problems with squatters at Red Rocket. I build a house on top of it. I have no settlers assigned there except whoever passes through with my supply lines. The only thing there is codsworth, and he just stands outside doing nothing but squawking his head off. The best thing to do is just not to have any settlers there. and if some just show up, assign them a supply route so they are never there.
From what I'm understanding, I think the ones he is referring to are just random NPC's..... which if you are a minuteman is kinda cool. "Hey, we can rest up as soandso's house."
And if that is the case, you may not be able to stop them from being on your front door. From what I've seen, settlers have an uncanny ability to teleport to wherever they please.
On the note of killing them, I thought if you shot a settler the rest of them would turn against you? I've refrained from exacting any wasteland justice from fear of be swarmed by 20 well armed and armored settlers. The whole "people shouldn't be afraid of their government, government should be afraid of their people."
As Vexen said Graygarden. Never build a recruiting tower there because the original inhabitants aren't interested in things we humans like. It's one of the very few places to find some peace and quiet in the wasteland. Just keep a power armor frame and a few fusion cores around in the rare chance it gets attacked so you can jump off the overpass. The other spot is just south of Saugus(sp?) Ironworks. Lots of bad neighbors in that area though.
Put beds in a house other than yours and assign the settlers beds. Unfortunately if you have a beacon that probably means that new settlers will just constantly traipse into your house. The best thing is to make a settlement just for you and your house.. (it'll never get attacked.) Make a different settlement just for your companions. (Sanctuary is probably the easiest for that.) .. and then make a completely different settlement for wandering settlers.. who you can care about or not care about.
Got rid of this issues by making the entrance to my sanctum have less than perfect pathing and the filthy hired hands can't get to the good stuff....
They'll just clip through the floors if there's no direct path. They'd still use the red rocket beds and house but would not climb my first set of stairs to get to house which was on the roof, they would magically teleport, clipping through the walls... I had to create a set of steps that directly connected to a floor piece and then they would use the steps.
If you don't want settlers there, send them to another settlement, and remove all food and water from the settlement.
Settlers have spawned inside my home at times when I fast travel. Plus as above they can clip occasionally making it all the more difficult to keep them out. Why couldn't we have a player bed and containers so NPCs don't steal or squat in our houses.
My character's home base is in the Red Rocket and the only others who live there are Codsworth, Dogmeat, and whichever other companion is tagging along with my character at the time. Dogmeat is either inside or roams just outside his house in the garage, and Codsworth just hovers around outside making various comments. Current companion mainly walks around, uses the crafting stations in the garage, or sits on a barstool at the bar drinking. Current companion never uses the bed or goes in the room. (I made the room that had the desk and file cabinets into a bedroom/private study.
Every single one of my supply lines from other settlements comes through the Red Rocket, so there are settlers and provisioners constantly passing through with their Brahmin, but not a single one has ever set foot inside the Red Rocket. Sometimes I might find a Brahmin inside stuck in a hallway, but its gone the next time I go back. None of the humans (or Greygarden provisioner) are ever in there though. My power armor in the garage has no fusion core just in case, but no one has ever gone into any of my storage chests or uses any items.
I've set up defense, water, electricity, but no food or beacon. Super mutants attack it all the time.
Other than moving furniture and workbenches around, I haven't built up any extra rooms or blocked off anything. The only issue has been companions always going in and out of the doors and never shutting them. Not sure why others are having these settler problems unless they somehow invited the settlers to come live there since I haven't seen a single settler other than passing provisioners.
I protect my privacy the same way I protect my Power Armor.
I put a wall up in front of the entrance so that you can only get in if you hit the "V" key and move the wall yourself.
No one and nothing gets in or out without my say so.