Why have males often been considered superior over females throughout history instead of vice-versa?

The answer for this depends on who you ask and their gender.

One view:Apparently because men tend to have hard-wired ego needs that women don't have. They are more aggressive, and more likely to assert themselves. Often, there are women-only groups because women tend to have more of a voice in groups when it is just women because they don't have to compete. In mixed group dynamics, men will speak over women and women will usually let them, since it is not in their nature to challenge things. Now, take that dynamic to life in general and to law and political science. First guys stepped over women to do things and then confused a lack of objection with consent. The women were not interested or not in a position to take whatever role. Then they went further and shut women out of those areas. That is how it is with male nature, and it isn't even intentional. They have this need to compete, dominate, and push limits that women tend not to have, and when you lack such traits, it is hard to perceive a threat, let alone counter it, so thus you have status quo.