Just why?

In some cases it's just the craziness like schizophrenia that Nightkin have and the Nightkin at Novac seems to just hear them mooing and turns it into something else. The stealth boys mess with their brains, so there's a lot that you can attribute to that or that might be revealed in a later game.

Lol imagine to them that if a brahmin makes a sound they think it says 'I am your god, kill in my name'

Nightkin are kinda-er hella crazy so...

I remember when I was doing that ghoul quest and you meet the one who worships the skull...man

A part of me feels bad for them though...andddddd a part of me loves shooting em in the face with a hunting shotgun

Perhaps the one gunning down Brahmin is just trying to save the rest of his kind from being tricked by false gods then?

Monster! Nightkin are our friends! They need our help. Always go for the cure.

Hot lead cures all problems!