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Personally, I wish I'd had OmniFocus in college. Maybe I'd have better productivity habits now.

Whether you do a folder per course with a project per assignment, or a project per course and action per assignment probably depends on the assignments. 'Write a researched essay' probably is a project, or at least a group of actions.

If I'd had contexts in college, I would have had:
@reading
@dorm
@computer
@main campus
--> @graphics lab
--> @library
@south campus
@people
--> @parents
--> @roommate
--> @prof X
@quiet

I found geographic locations far more relevant than 'what kind of work am I doing' categories. The number of times I got back from class only to remember I should have picked up something while I was down near my prof's office -- argh!

We've tried to make OmniFocus an app where you can ignore the power tools (like perspectives and the mail clip-o-tron etc. etc.) until you need them. If the basics of projects and contexts are making sense to you, you should be fine.