No they aren't. Not sure what "Original Fallout" you're talking about, but in the first Fallout the BoS can actually help you attack the Super Mutant infested military base. Don't recall anything they did to make them enemies. They give you quests, you can even join. If you're karma is high enough, you'll even get a suit of Power Armor. Hardly the things "enemies" would do.
I only played Fallout 1 once after F3, but I recall them helping you. They're jerks in that they trick you into going into your "BoS initiation" by entering a rad infested area with Supermutants (I think...) thinking you'll be killed.