Why must Barbara suddenly live in a world where her father and all these big bad men set out to stop Barbara from doing what she wants to do?
Well, on a meta level... Frank Miller. Batman got reinvisioned a bit post-Crisis as an emotionally incompetent, cripplingly deranged, Lawful-Evil-half-the-time asshole who's obsessed to a clinical degree with control over his city and all vigilante activity therein. Making it no longer possible to have a story where he's anything but a stumbling block in any aspiring vigilante's way. There was no way to adapt the Batgirl story - in which *she* chooses to be Batgirl, rather than him choosing it for her as he did Robin - without either making them adversarial or contradicting the New Batman. It would have been out of character to make Bruce anything but a massive mindfucking dick to her.
And once you do that, there's no justification for an intelligent, confident woman like Babs to tolerate him unless she has no other option, so if you want her to still be Batgirl in spite of his shit, you've got to make everyone else a dick too.
It's character driving story, which is absurdly rare in comics, and BG:Y1 pretty much singlehandedly demonstrates why: because comics are fond of tossing around characterizations that, if you actually obey their logic, become unworkable.