I'll be the first to say I've had some outstanding student-athletes in my classes at A&M, VT, and my current D-III school. And I've had ones who gave me pause about admissions standards. The latter, unfortunately, outnumber the former, especially in high-profile programs (football and wrestling at my current institution).
How do they then pass academically? Well, at the D-I level, there are all these tutors, employees of the athletic departments, whose job is to ensure they "succeed" academically. And some of those definitely cut corners, as we have seen. At D-III schools, however, they just limp along until they flunk out.