At the beginning of Doctor Faustus, the not-so-good doctor thinks the study of religion is a plain old waste of time. But we're betting that by the end of it, he'll be singing a different tune altogether. See, through all his conjuring exploits and exotic travels, Faustus just can't escape the subject of religion. He finds himself questioning the nature of hell and salvation, and even winds up smack dab in the middle of the papal court, where he does his fair share of mocking the Catholic church. Yet while religion follows him, step-by-step on his slow journey to eternal damnation, we can't help but think that Faustus never really gets just how important religion really is in his life, or the role it will eventually play in the fate of his soul.
Doctor Faustus is clearly pro-Protestant because Marlowe does just about everything he can to make Pope Adrian appear ridiculous.
Faustus makes Pope Adrian look a fool, not Marlowe. So the play is not pro-Protestant or anti-Catholic. It's just anti-Devil.