Any religion involving daily soulless repetition, lack of independent thought or theory, or self-sacrifice in preservation of the hierarchy is a cult. Catholicism, Mormonism, Christian Extremist... what-have-you.
Much of Final Fantasy's religious undertones can be seen as more or less references to Greek mythology which in itself I believe was the second longest lasting religion beside Christianity. Many powerful men (powerful for being born to kings) claimed more power by proclaiming themselves the progeny of some god. Hercules was a soldier claimed as the son of Zeus. Alexander of Macedonia claimed to be the son of Dionysus. Is it any wonder then that the Romans in power in Jerusalem balked at the idea of a poor carpenter being the son of God? Even the Hebrew people were skeptical.
I think Final Fantasy VII shares this theme the most. Sephiroth thinks he is literally the son of Jenova but he is genetically the son of Hojo and Lucrecia. Having been infused with Jenova's DNA during conception, his body merely developed a tolerance to its power and over time, his mind began to succumb. Even his followers are simple experimental subjects injected with Jenova's DNA by Hojo. But then where does one draw a solid line between scientific certainty and religious faith?