Of course men and women should be equal in society. That does not mean they are or that they have always been.
For this topic you really have to consider so many factors: women in the US have equal rights under the law, but that doesn't mean that every woman in America has equality. Laws are a great start but they can't change attitudes.
As for your references to God: I think you need to consider the difference between religious dogma and the rules of religion made by man, and what God "says". Each of us believes different things about our creator. The reason religion can be so divisive is that there is no proof either way. Scriptures and other religious writings, were written by the hand of a man. Whether you believe that there was divine intervention or not is a matter of personal belief. No one can say that God says women are inferior. You can believe that, but you have no proof.
Additionally we have to consider social constructs and how they have changed and continue to change over time. Matriarchal societies are not nonexistant and often in male dominated societies woman find alternative ways of exerting power. Women in China had no political power for centuries but their writings and art, and their influence within the home has had huge affects on Chinese Society. Look at the salons in Europe during the Renaissance and Enlightenment period. Women almost always ran these and the most prominent political, scientific, artistic and other ideas of the time grew in the parlors of these women, most of whom were still politically disenfranchised. In modern America the increase in single parent households means that there are whole families and kin units and communities being run by mothers and grandmothers and aunts.