The plot and thematic content of Dr. Faustus is certainly weighty and--truth be told--a little less than optimistic. On one hand, the more comedic scenes are ways to address some of those same themes and plot elements in a lighter way that is, perhaps, more accessible for many of the members of Marlow's audience.
Much like Shakespeare a century or so before him, Marlow had a difficult task in writing a play that would speak to both the members of nobility in his audience and also to the commoners who were there as well. Marlow knew he must keep the commoners engaged in the play and entertained. If he didn't, they would most certainly become unruly and interrupt the performance. The comedic scenes are included as one way to help keep the audience entertained.