Why do some languages have male and female nouns?

The answer to your real question 'how did this feature of language come to exist?' is so simple. Just like any other linguistic or grammatical nuance, in any language, we say things a certain way because THAT'S THE WAY WE HEARD IT! People say a certain thing a certain way long enough it becomes a rule. I am sure someone has published their thesis on the influences of colonialism, religion, etc.... on the grammatical rules of a particular language, but it will tell you the same thing I am. We hear things a certain way BECAUSE of all of those influences. Humans don't like change so we stay with what is comfortable. Next thing you know, you got a rule.