The script indicates that Neo is having problems coping with this one as well. The very short answer is that your prejudice (and his) prevent you from seeing that independent beings of free will and intelligence are perfectly capable of falling in love, procreating and striving to protect their offspring, all without the mucky messy business of squishy brains and thrusty groins.
It's clear that although their Rama and Sita's "love" is of a qualitatively different basis, Rama refers to it as thusly when inhabiting a human-shell and talking to a human.
Neo struggles with the idea of a Machine loving another Machine.
RAMA: You do not understand?
NEO: I just have never...
RAMA: Heard a program speak of love?
NEO: It is a human emotion.
RAMA: No, it is a word. What matters is the connection the word implies.
He reads Neo's code.
RAMA: I see that you are in love.
Neo feels awkwardly exposed.
RAMA: Can you tell me what you would give to hold on to that connection?
Matrix Revolutions - Original Screenplay
Interestingly, it's when machines go rogue that they begin to exhibit emotion such as love and hatred, implying that these "human-like" emotions are very much frowned upon by the machine mainframe.
AGENT SMITH: I don't know. If I knew...
Agent Smith hides his knotting fist. He is becoming angry. It is
something that isn't supposed to happen to agents.
AGENT SMITH: Leave me with him.