Not quite sure what you mean by "make-up classes" in this context. During regular ac year, if mids are traveling for sports and activities, they are responsible for working with instructors to get assignments, stay current with coursework and take missed tests.
Summer school is either voluntary or involuntary. It is a 3-week block. If a mid is in academic trouble, he/she may be directed to repeat the course during summer, if the Academic Board determines they should get another chance, or lighten their ac year course load by taking courses during the summer.
Many mids take summer school voluntarily, to get ahead on their matrix to set them up for the VGEP Master's program which starts spring of 1/c year (search other threads), to support a double major, to ease ac year course load for various reasons, etc. Many decide the quiet summer school routine, while intensive in one subject, gives plenty of time to work out, relax, do water sports, explore the local area, enjoy beach weekends on the Eastern Shore, play golf, especially if they find their hometown friends scattered and not much to do back home. The Yard is relatively quiet in June, then gets busier. The summer schoolers are all together in one wing of Bancroft Hall, with summer campers, plebes, transients and other summer blocks elsewhere. Caveat: involuntary mids typically have less liberty than voluntary mids.
Plebes usually can't imagine sticking around USNA for school the first summer, though many do, especially if the Chem and Calc Plebe Killers run true to form.