Tom and Maggie represent opposite sides of many themes in The Mill on the Floss, and gender inequality is no exception. Basically, men had all the rights in the Victorian period. Tom bosses Maggie around accordingly, and has advantages that Maggie does not, especially educational opportunities. But women aren’t the only ones who get a raw deal here. Men can't always act the way they want either. The world of this novel has a very narrow view of how women and men should behave. And men like Philip, who is artistic and sensitive, are derided as "feminine" and considered "unmanly," just as Maggie is often considered scandalous for her bold nature.
The differences and conflicts between Tom and Maggie actually represent the gender divisions and issues that plagued Victorian England as a whole.
Maggie was often treated worse than Tom when they were growing up because she was a girl.