I haven't read most of those fics. Maybe some of the writers are using poetic license, but given that the show doesn't tell us how often or how badly Brian was a abused it's maybe fair enough.
I imagine that Jack stopped being physically abusive towards Brian somewhere in his teenage years, partly as Brian was probably able to avoid Jack much more easily, and partly as he got physically bigger himself and therefore able to defend himself.
Probably someone has already mentioned this, but Brian tells Justin he was abused too, around the time in S1 when he tells Brian that "a boy needs a father...".
There's enough support for the idea of Jack as drunken and physically abusive, so that's what he was. It's not made up by the fandom. We just don't know how frequent or how severe the abuse was, so I don't mind the poetic license. Well I wouldn't mind it if I actually read it.