anyway i don't think anyone hates the BoS (well maibe Gabe

) they are just over used and they are just fine in NV has they are you can totally disreguard them
I know, it's not like the Brotherhood are like "hey were everywhere." There sitting in a bunker and that's it (unless you do their quests, then they supposedly patrol the highways on occassion but you never actually see them patrol).
You can totally playthrough the entire game and basically ignore them, you may have to make a stop to kill them if your faction requires it, but after that, that's it.
And nobody
FORCED you to work with the Brotherhood in Fallout 3, you can actually work against their interests by lacing the purifier and pretty much destroying them by calling an orbital strike on the citadel.