What is the audience supposed to think of Faustus after the chorus?

  During the chorus, the audience is urged to reserve judgement on Faustus ('To patient judgements we appeal...') which gives the impression that he may have done some pretty unacceptable things but perhaps that he had justifiable reasons that we could sympathise with. The writer also mentions his infancy in the present tense, saying '...now is he born...' , to garner a sense of sympathy.

  With the accounts of Faustus's education that follow, it is easy for the audience to see Faustus as an intelligent and honourable man who has worked his way up in the world. The chorus declares him a man who 'profits in divinity', something that would have been respectable through the deeply religious ages in which our audience lived, and titles him a 'doctor' who happened to study a prestigious university attended many wealthy kings which commends his intelligence since he did not use his non-existent wealth to get in.

  However, the lines that come after this cast a less than favourable light on our protagonist. It is described that abundance of knowledge has caused him to become 'swoln with cunning, of a self-conceit...'. The writer then compares Faustus's tale to the fate of Icharus.
  (According to Greek mythology, Icharus was the son of Daedalus, the craftsman who built the labrinth in which the legendary minotaur resided. Daedalus and his son were imprisoned in the labrinth as punishment for giving Ariadne the clew that she used to help Theseus kill the minotaur and escape the labrinth. In order to escape, Daedalus built a pair of wings out of feathers for both of them and warned Icharus not to fly too close to the sun. But Icharus, giddy with his newfound sense of freedom, did not heed the warning and flew too high -of course! The wax holding the wings together melted, dropping Icharus to his watery death by drowning in the sea.)

(The Greeks like their mythical characters naked apparently. Though I have no idea why anyone would even consider that Icarus would decide to fly naked...)

  This would be construed as a metaphor for Faustus, in his pride, trying to rise too high, too close to God, and being punished for it. The audience would also note the phrase 'heaven conspir'd his overthrow' which implies that the punishment is one from God, and perhaps not entirely his fault.

 The chorus moves on to the subject of necromancy and magic, two ideas that would have been considered unholy or blasphemous, perhaps leading the some in audience to condemn him or at least begin to judge him unkindly. The last line of the chorus reinforces the idea of his intelligence with the mention of Faustus being in his 'study'.