In-universe, presumably most of the Doctor's incarnations have just gotten along better with women.
Behind the scenes, having a male lead and a female lead is a standard, and successful, formula. Doctor Who has at times blindly followed that formula, while at other times it's actively subverted it (as with Leela being the "action hero" or Zoe being the brilliant problem solver).
Also, especially in the classic series, companions did a lot of screaming in terror, and actresses tend to be better at this than actors.
Plus, Jamie McCrimmon notwithstanding, men don't look as good in those short skirts, and you've got to keep the dads watching along with the kids.