Dawg, in a world controlled by machines, an act of love by human beings is an act of resistance.
They weren't using rubbers man, having kids itself is an act of resistance. In Zion.
I don't think you really vibed with the Matrix if you just thought it was some kung-fu, cypherpunk fever dream. It's about the war between humans and machines, and in that context, the sex scene was necesssary.