Caesar's Legion really handled this best: despite the fact that a very, very large chunk of Legion society is founded on slavery, there are average citizens under legion rule. Merchants, traders, villages, etc. They're not quite slaves, but they're not quite free/citizens at the same time. They're servile, and serve the Legion without question (because anyone and everyone knows unlawful acts get you the Lanius/Nipton treatment). If Mars, the God of War blesses the average "vir in urbe Flagstaffis" (man in the city of Flagstaff, yay knowledge of Latin!) with a fortunate life, then perhaps he will not have to answer to the commands of a Legate or Legionaire in his life. If he is truly lucky, perhaps he can live out his days serving Caesar as a costodem viae (super rough translation of guard along major roads)-----but if he is commanded to obey anyone with authority, he will do so without question, without hesitation.

As much as I hope the organization will reform in the future, I'm always reminded of Veronica, an estranged and likely excommunicated member of the essentially extinct West Coast BoS. As she tries desperately to steer her chapter away from the path of dogmatism and fanaticism, she is faced with opposition at every turn. After venturing on an impossibly dangerous quest to find a piece of technology to convince the Elder to change the chapter's priorities, this scene plays: https://www.youtube.com/watch?v=84E1HVsiDTQ (4:20-7:55)

To respond to your question, I guess it has to do with what the natives of a region consider as important. Paul Pembrook and Henry Cooke seem far more concerned with the shady dealings between Diamond City and Goodneighbor than the deathclaws, gen 1+2 synths, and various beasts of the Commonwealth. Pretty much every single companion in Fallout 4 highlights the failed relationships or disappointments they've had with themselves/other people, rather than venting about the dangers of the Commonwealth. Even Piper "alarmism" Wright is far more concerned about the lack of commitment to duty to one's job/role than she ever was about Alpha Deathclaws. The argument could be made that to them, Deathclaws, Mirelurks, and Synths are just part of living, much like rabies-infested vermin, mice, and feral animals in real life are just part of living----but nobody's calling for a purge in either case(except the Brotherhood/Enclave).