Firstly, the feature of "gender" is not only restricted to "feminine/masculine" or "feminine/neuter/masculine". This is something quite European. While gender systems outside can be very different: "inanimate/animate", "fruits/people/animals/inedible things", or the extremely expansive systems in some of the Bantu languages. To the question itself, however.
Disclaimer: I am not a professional Linguist, so I could very much be wrong. I encourage anyone to correct me.
Gender systems developed as they had use. Some were distinguished things by "What is it?", as with the non-European examples of gender systems. It is easy to see why this could be helpful. Especially for pre-literate communities. While in other gender systems, that are mostly arbitrary: they could have been used to distinguish between similar sounding words. Or they could have held a similar role to the most concrete systems, as I'd mentioned, but simply grew archaic in meaning.