It is the mind of Faustus, and by extension the mind of Renaissance humanity, upon which Marlowe's play focuses.
In both Faustus's character and the scenario developed throughout the tragedy, a series of conflicts are shown to us that are emblematic of the zeitgeist of the sixteenth century. One issue is power. Are men justified in seeking worldly power? Machiavelli's The Prince had become a central text of the era, and its ideas about power galvanized a debate that still hasn't ended. Marlowe poses the question of the legitimacy (or lack thereof) in Faustus's wish to become, in effect, a super-being. Do people (even in the absence of a literal devil such as Mephistopheles) at least metaphorically "sell their souls" in order to achieve power? Arguably, the "message" of the play revolves around this question of earthly potency versus spiritual good.
If we are talking more directly about the conflict that takes place within Faustus over the issue, it's clear that Faustus has been motivated by some sense of insufficiency in normal life—in his case, the life of a scholar. His accomplishments are inadequate for him, unfulfilling and incomplete. He even anticipates Macbeth in his feeling that life as it has been is empty and meaningless. He wants more and more power to fill this emptiness, striving for what no man has had or should have. In doing so, both of them—Faustus and Macbeth—defy the laws of God and man.
Their defiance is punished, but to some degree this is misleading. Though Marlowe (and Shakespeare) predate the Enlightenment by 150 years, the themes of both Doctor Faustus and Macbeth hover on the precipice of the rejection, or at least the questioning, of the absolute authority of religion. The Protestant Reformation had already thrown into doubt and confusion centuries of European unity on religion, and Faustus's plunge into heresy by his pact with Mephistopheles is a private extension of this breaking away from the safe solidarity with tradition. By putting his own soul into peril—apparently intended quite literally by Marlowe—Faustus is also like an explorer gone too far, venturing into an unknown realm, the "undiscovered country" from which there is no return. So, we see a drama in which themes of power, the meaning (or absence of meaning) in earthly life, religion, and exploration of the unknown converge in Faustus's mind as a metaphor of the European consciousness of his time. Doctor Faustus is a study of both this inner mind of its protagonist and of the mind of an entire people.