This is an impossible question to answer with complete certainty. We can never prove why societies have tended to see women as inferior.
My theory is that this tendency dates back to the days in which so much of what was necessary for work and for defense required heavy physical labor. I would argue that our ancestors all lived in societies in which much of the work of getting food and defending the community simply had to be done by those with the greatest amount of physical strength. I believe that from that, we got the idea that men are superior to women simply because physical strength was important and men had it.
There are certainly potential holes in this view of the issue, but I think that it must surely do a great deal to explain why male dominance has been so pervasive in societies across the world.