Neo represents every teenage boy; you are leet, you discover something secret but world-changing, you are initiated into a new world and the scales fall from your eyes. It is a metaphor for becoming an adult.
Cypher represents defeatism, the impulse to give up and run away and be turned back into a little boy. He is the embodiment of the moment after you are rejected by a potential partner for the first time. I want to go home.
Morpheus, by contrast, is the father. He is the one who affirms Neo's maturation and believes completely in him.
Why does Cypher betray Morpheus? Because Morpheus' role to support the rite of passage into adulthood is worthless if it is better to remain a child, and Cypher rejects the truth. Also, as an allegory it illustrates how futile it is to attempt to return to the child state; once we know, we cannot unknow.
Following the logic, this allegory is telling us that hedonism (satisfying the senses) is not sufficient for happiness; the story embraces purpose (and even ideas of destiny) over sensuality.