Superman is space jesus. Jor El gave us his only begotten son (whom is powered by the sun) to 'save' mankind, and to live as an example for us. The Kent's are Mary and Joseph, a couple with no child, virginal.
The bad guys are science heavy. They wear technology, saying things like evolution makes them superior because they have no morality (untrue). Jor El, conversely, as a 'scientist' flies around on an alien bird and gives his son a natural conception because science is bad. Jor El points out that using science to mine the core of their world led to it's destruction. Jor El is then the heavenly spirit, walking around the ship giving Kal El advice. Right there you have the father, son, and holy ghost.
As a boy, after saving the school bus, the lady came to suggest that Clark was godly/gifted. In his vision, he is even on an apocalyptic mountain of skulls. The movie repeats themes of faith, trust, and choice/free will.