Well, I would say that there's little difference... however in "What chapter are you studying?" the emphasis is on "now; at the moment;" - probably at the moment of asking the question.
"What chapter do you study?" is more general and may refer to not specified time, as if the act of studying takes place "all the time", not necessairly in this very moment but in general; a person who studies, probably did it 3 days ago, does it today and will do it for some time in the future,
Correct me if I'm wrong.
Interested in Language