But, but.
Why throw away self preservation in the name if progress when your heavily armed nigh invincible daughter is right behind the jerk ass harassing you?
The problem, then, is not with the story as such, but with the 'heavily armed nigh invincible daughter'. It's a problem common to all these games, be it FO3, New Vegas or Skyrim, namely that eventually (and usually pretty quickly) the player becomes a living god for whom the petty concerns of mere mortal NPCs are trifles that can be settled in a matter of seconds. The story, though, is not (and, realistically, cannot be) written with that in mind. The Enclave are meant to be a terrifying threat to the Wasteland, not a bunch of idiots who can be massacred by the dozen by a kid who's just left a vault. I don't think that is going to change, either, as the bulk of players like levelling-up and being heavily-armed and nigh invincible.
My favourite character has an Endurance of 1, wears no armour and has no resistance-boosting perks. For her, that scene was very real as, despite the sophisticated weaponry she had at her disposal, there was no way she could have helped her father had he opened the door: in a straight-up toe-to-toe fight against 3 Enclave soldiers she'd have been dead in about 2 seconds. I think that is the kind of situation the story is intending to convey.
I think the best way to approach these stories, and indeed the whole world(s), is to consider things from the point of view of an NPC, not that of the god-like player. Why, for example, have people from Megaton never thought to go and get rich by taking over Super-Duper Mart? Because real people die when they get shot, and real people starve in environments like the Wasteland when they're injured and can't work. It's not worth the risk.