I'm playing as a good guy. I'm neutral or liked by everyone except Fiends.
However, on first encounter with the Brotherhood, they're hostile and kick my ass before I can even get close.

Are you wearing NCR armor?

I WAS wearing the Van Graff Combat Armour but I also tried just wearing the Wasteland Doctor fatigues. They kick my ass on sight.

Sorted this now. They only kick my ass if I encounter their patrol at night outside the bunkers.
If I go into the bunker in the day, it's cool.

I got attacked when I had NCR Armor on I then took that off after about six months past and they hate me but hey I use for getting money fast people want that power armor

Do you have Boone with you? that can be a problem if you never went in the Bunker nor active related quest.

boone well i decided to keep him outside but that could have something to do with it

maybe having boone just piss off BoS too... like Legion.... if you have boone as companion eventhough he's not near Legion will attack you

no it's not Boone, i did the first of their quests last night with boone in tow and it made no difference, unlike with the legion when he threatened to kill all of them :gun:

Companions don't matter. They don't care even if you bring Lily inside. Boone is neutral to the thing, just like other guys they could potentially be pissed about, Gannon especially.

It works other way round too, I had Veronica parade in her factional Power Armor in front of NCR and others whole day and noone minded it.