These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Major Thomas Magruder is feverishly seeking a legendary lost city of gold called Quivira, and murders or tortures anyone who gets in his way. His defining moment came in a flashback to years before the events of the game, when he came to a small homestead out in the plains belonging to a benevolent doctor who helped the nearby Apaches. When the Apache chief tells Magruder that his lust for the treasure will lead to his doom, he coldly shoots him, then beheads the doctor. When one of his own soldiers protests his actions, Magruder shoots him, too. In present, Magruder simply attempts to wipe out the Apaches and whoever else he deems an obstacle to his hunt for gold. Magruder is a man singularly devoted to satisfying his own greed, no matter who gets in the way.
Magruder's right hand man, "Reverend" Josiah Reed, is a monster in his own right. Reed initiates a massacre at the game's beginning on a steamboat that takes the life of the hero Colton White's adoptive father Ned. When a prostitute named Sady refuses to give Reed answers, he throws a hatchet into her head and has the entire crew massacred. Reed is revealed to be an unhinged lunatic, every bit as bad as his violent boss. When he captures a prostitute named Jenny, Reed pointlessly slits her throat to let her die in front of Colton.
They Wasted a Perfectly Good Character: Sergeant Hollister and the Renegades. The idea of an entire fort of U.S. Army soldiers having gone not only rogue, but totally insane ala Apocalypse Now, seems like an interesting concept to explore, except it's never explained why they're like that, or why they would work for Reverend Reed, who is in turn working for a former Confederate officer (Thomas Magruder). Indeed, if it weren't for their association with Reed, they would just seem like a mere Wacky Wayside Tribe.
And we don't know much about Hollister himself, apart from the fact that he led the attack on the steamboat at the beginning of the game (even though we don't actually see him do this) and he's not even introduced until much later in the game, only to be killed off two missions later. If anything, it's as though he was only introduced so that the game could have a boss battle in which Cole re-obtains Ned's rifle.