Protestant Elizabeth succeeded Catholic Mary in 1558. There is a strong anti-Catholic vein in "Doctor Faustus", for example in the Pope scene (Scene 8).
Doctor Faustus: AS & A2
The Puritans championed free speech and individual conscience. Faustus embraces free speech, but parodies the obedient churchgoer in echoing the Evil Angel.
Following classical thought, humanism embraced reason and human dignity. Faustus uses his reason to challenge the existence of hell and to choose his destiny.
These featured an Everyman figure who transgressed but was eventually saved. Marlowe uses elements of this (e.g. Seven Deadly Sins), but subverts the tradition: Faustus is damned.
Marlowe's contemporaries believed in a divinely-appointed hierarchy starting from God and moving down to the common man. Faustus tries to usurp this divine order.