Why do some languages distinguish between "male" nouns and "female" nouns?

Most Indo-European languages distinguish between masculine and feminine (and sometimes even neuter) nouns. This is because the Proto-Indo-European language distinguished between these. Originally, masculine, feminine, and neuter nouns where not divided so arbitrarily, but as mythology affected this aspect of the language (things ruled by goddesses where feminine and by gods masculine), the gender of objects began to make less and less sense.