My reputation with the Brotherhood is "Idolized", except for this little matter of trying to shoot me on sight anytime I get close to one of them. I'm not wearing any faction armor and I'm not using any mods.

In what location are you when they start to shoot you?

Hidden Valley. Either in the bunker or outside of it when the patrol is there. Santos at the safe house has tried to kill me as well.

Might be this little matter of me killing everyone in the bunker. Except most of them re-spawned, including a few of the "named" characters. Vengeful ghosts perhaps?

Wouldn't the better question be "Why am I still idolized by a faction when I've wiped out an entire base owned by said faction?"

They got better!

BUG! KILL IT WITH FIRE!