What people underestimate when it comes to running an entire college is the sheer cost of keeping everything going. It's not just paychecks to the professors but the staff. It's not just the buildings upkeep but the utility bills of all the campus building. It starts to add up into a very large, expensive sum.
Schools, while they're there to teach their students and benefit them also have to bring in new students, new knowledge. There's recruitment to worry about and being able to provide for their students, not just for disabilities but even dietary restrictions. Schools are an institute. A giant organization that takes countless of people to keep running and train the new recruits. Public or private they almost always need money.
Part of the reason why students might feel like they aren't getting everything they could from what they've paid is because of the student body. They are one student out of hundreds on campus or maybe even out of tens of thousands. That then brings up the problem of favoritism. Leftover money is much different than scholarships or grants that can be given to students who are applicable for aid or have won the grant. This money can't just go back to the students because if the amount returned would be miniscule.
Leftover money is usually allocated to fund something else on the campus like the clubs or it's used to entertain the students. Things like comedians or bands coming to perform on campus, paid for with that leftover money. While students would no doubt prefer having it given to them, schools can't just return the money because it leaves the question of who should they give it to and as much as every student would like to say themselves it's much less complicated for the schools to plan something for all the students instead of surprising only a few.