1) Gordon isn't in charge during Gotham Central. It came about because of Gordon's retirement.
2) Romy has serious issues with Batman because her previous partner who she had unrequited love for died possibly due to Batman's actions.
3) She shot him.
4) Batman's opinions of Gotham's cops has deteriorated a bunch since Gordon's retirement. Out of nowhere, they were no longer giving Batman as much leeway and pushing the boundaries of their relationship.
5) She shot him. He's supposed to be completely calm about that?