I've encountered the same thing, and have noted this seems to be more prevalent in situations where 1) I am unfamiliar with the travel route and/or 2) there are lot's of twists and turns.
You have the advantage in that your commute to/from school will typically follow the same route each time. The key, I've found, is to first become familiar with the route: where are the sharp turns, steep inclines or declines ... and where are the frequent stop and start sections. You'll know you are "familiar" with where these things are in your route if you can successfully sleep through the trip yet still wake up in anticipation of ... say a stop or two before ... your stop! ;-) This happens because your body has learned to subconsciously anticipate and acknowledge where and when those changes in the travel direction will occur.
Once you've mastered your route you can successfully read without becoming motion sick. You may have to pause to look up and just watch the road during the tricky areas (sharp turn, steep incline/decline, frequent stop and go), but should be able to resume reading during the rest of the trip without the motion sick feeling.
Hope this is helpful!