Even for guys not getting a monster signing bonus can still get good education guarantees from their professional contract (If you sign for $90k, we'll pay for tuition for your undergraduate degree as well).
Except there are a fair number of strings attached to that deal: http://mlb.mlb.com/mlb/official_info/scholarship.jsp?content=guide
Plus, the player no longer gets any help getting into the school of their choice. Nor do they get tutors, preferred enrollment slots, and other perks that student-athletes get at most schools.
All in all, it is a plus, but not a slam dunk deal.