That's only for the first time they harass Veronica. When you actually want to help her join the Followers of the Apocalypse at the Outhouse, you have to wait a day before returning, then you find that the Brotherhood killed everyone there because Veronica tried to sell them out. I used Terrifying Presence on them then, and they all went into flee mode, and I slaughtered them all.
Going back to the bunker was revenge for them killing Followers. I love the Followers of the Apocalypse. Motherfucking cocksucking Paladins!
Now I know exactly how Tom Anderson felt.