What you have asked covers the supreme theme of this play by Christopher Marlowe, Dr. Faustus, which is the inner conflict of Faustus. Marlowe's hero goes through the dilemma throughout the entire play. It is this conflict which turns Faustus into a round character, and successfully, makes him a tragic hero.
Faustus, who is a renowned professor in a German university, a prolific scholar and a skillful physician who helped his town to get rid of plague, seems to become more proud out of his fame and achievements. He tends to practice necromancy now. What he has achieved till now could not give him satisfaction; he wants more. And, he thinks it is black art which would help him to reach the peak. Thus, he chooses self-willingly the wrong path for himself, and sells his soul to Lucifer via an agreement. This ambitious man abuses his knowledge and skills being distracted. He denies God and focuses solely on earthly pleasure. He says to Mephostophilis that he will spend his life "in pleasure and in dalliance" and his preference to sensuality than to spirituality makes him a villainous character. But, Marlowe shows brilliance in giving this villainous character a diversity.
Faustus, though driven by his freewill, many a times tries to call Christ. His attempts to repent and coming back are clearly shown when he is saying: "Then fear not Faustus, to be resolute..." or "be resolute:/ Why waver'st thou?... turn to God again" or, when he sees an inscription on his arm which tells "Homo fuge!" and then, he falls into deep thoughts whether he should pact the deal or not. While selling his soul to the devils, he calls Christ: "O Christ, .../Help to save distressed Faustus' soul." Even when he reaches the end of his life-time, he still hopes that Christ would forgive because he knows: "Christ did call the thief upon the cross". At the end, he realizes that, "no end is limited to damned souls".
A tragic hero is a human endowed with some extraordinary qualities, at the same time, possesses a hamartia or tragic flaw in his characteristics which will lead him to face heavy downfall. This Profound scholar Faustus, having excellence in his character, becomes a fallible man gradually, and his life results in terrible consequence because of his pride and ambition.
Faustus is not flatly a negative character, rather possesses really "an amiable soul", and this fact is implicitly depicted through his inner dilemma.