Because if there wasn't a loss of bowl/playoff games, schools would just pay the fines and replace the student advisers and faculty and repeat the process.
By the time the NCAA finds the offenses, the games have already been played. It's all about getting key (struggling)players through the classroom and onto the field.
The only way to make sure schools quit doing this crap is to keep them out of the money games. The un-involved athletes are simply a casualty of war. The guilt of unfair punishment is intended to help keep the coaches, faculty, and offending students from choosing the wrong path.
again, I think that is an outdated way of handling things. If that is the "only way" why does it continue to happen?