The answer to each segment of your question depends, as with many issues in literature, on the beliefs or the views which we, as individual readers or theatergoers, adhere to before we even experience Doctor Faustus. A religious person will probably see the play as a straightforward parable of man's disobedience and punishment, like a medieval reenactment of the story of Adam and Eve. Faustus is tempted by the devil, Mephistopheles, and as a fulfillment of his "pact," is condemned to hell. People not especially sympathetic to traditional religious doctrine might see this as the principal message of Marlowe's play but would recognize other themes, perhaps relating to human nature and the striving for something greater than the ordinary conditions of life to which we are subject. And those who are anti-religious would probably see Faustus's rebellion as admirable and heroic, viewing him as a symbol of man alone, justified in trying to break out of the conventional restrictions imposed upon us by religion and authority.
The fact that all these interpretations are credible shows how timeless the play is, but it also makes our task more difficult of trying to discern the message Marlowe himself intended. Probably the censorship exercised in the Elizabethan theater would have required Faustus to be damned at the end of the story, regardless of whatever Marlowe's deeper intent might have been. It's significant that from the very start Marlowe shows Faustus as a man dissatisfied, unfulfilled with his scholar's life and achievements. The portrayal attests to a deeper problem than simply disobedience or perversity. More than any other scene, the opening anticipates Goethe's treatment of the legend 200 years later. Even in Marlowe's approach Faustus is a man in search of some ultimate experience to tie everything together. In this he's a kind of hero, but the manner in which his quest is played out is anything but heroic. The ability to "raise spirits" Mephistopheles grants him does not seem the height of a soul's striving. And the end of the play doesn't seem merely tacked on in order to satisfy the censor or the religious authorities.
The deeper theme of the play is arguably portrayed in Faustus's final experience, his encounter with Helen of Troy. It implies that sexual fulfillment is Faustus's ultimate wish, not exactly surprisingly, but once it happens, there is evidently no sense of gain or completion. It's as if Marlowe's point is the transience, and ultimately the meaninglessnes, of the physical world. Faustus is left alone with his terror, his knowledge that his fate is something he cannot change. He is neither good nor evil, but simply a man isolated, a victim of his foolishness in spite of the quasi-heroic intentions that animated his quest.