Part of the reason that Marlowe's Faustus is tragic is due to our own susceptibilities and foibles that would compel us to do the same.  This is to say that Faustuts' tragic flaw was his greed.  Simply put, he believed that "greed is good."  His faith in greed, and acquiring knowledge and power through science, is something that ends up moving him to sell his soul and causing eternal damnation.  This is tragic because it represents the story of an individual trying to appropriate the world in accordance to his own subjectivity.  Faustus uses his freedom to overtake the world as his own world, and in his endless belief of his own greatness and talent, the seeds of his eternal damnation and tragic condition lie.  While the reader is able to scoff and deride him, there is much in Faustus that is similar to our own condition.  The endless faith in one's self, the desire for absolute power and control in our own circumstances, spreading this outward, and the greed for more in the belief of our own superiority are traits that apply to all human beings at some point in time within the right circumstances.  This desire to appropriate the world in accordance to one's own subjectivity invariably leads to the reality that every step towards its creation is a step towards its destruction.  These two life forces go together in such a setting.  In such a paradigm, Marlow's work is not a comedy as much a reflection of the human predicament, making it tragic.