Since when? Most of the show's main villains have been female -- Astra, Indigo, Lillian, Rhea, Reign, Mercy, Eve. And of the primary male villains/antagonists like Maxwell Lord, Non, Hank Henshaw, Morgan Edge, Ben Lockwood, Manchester Black, and Lex Luthor, I don't think any of them besides Edge have been portrayed as sexist; they've mostly been motivated by power or revenge or anti-alien racism.
Female empowerment doesn't mean the stories have to be about fighting sexism. It means the stories move beyond sexism and women can be both the heroes and the villains. And female empowerment is male empowerment too, because men limit themselves through misogyny (e.g. by condemning other men who display "feminine" traits like empathy). So there's plenty of room in a show about female empowerment for male characters who are empowered by not being sexist, e.g. James, Winn, J'onn, Mon-El, or Brainy.