Hi there,
I'm not sure where in the South Loop you are located but there's a great coffee house, off the beaten path located in Pilsen.
Efebos Cafe, located at 1640 S. Blue Island, is a spacious cafe that at once feels quaint and homey. Local art is on display and it seems to change every few weeks. They are also an internet cafe, so there are computers and printers located on one side of the room.
I think Efebos gives the venerable Pilsen institution, Jumping Bean, a run for its money. Efebos has delicious sandwiches (try the turkey) and pastries, and it would surely fit the bill of a quiet place to study. There is a large room up front with the usual couches and tables, and then a smaller room in the back which is great when you need some quiet. Even when Efebos is full, it's still pretty quiet. Their eclectic music selection is great background for anything.
I would like to recommend another place, located on Madison Street (north side of street) between Racine and Sangamon, but I cannot for the life of me remember its name. Again, great atmosphere but a bit busier. If someone knows the name of this place, post and remind me, I can't think of it!
Efebos Cafe
1640 S. Blue Island
312-633-9212
Jumping Bean
1439 W. 18th St.
312-455-0019