I'm not in college anymore, but carry my 13" MBA around quite a bit, both in a backpack and without. Its plenty portable, and the perfect size in my opinion.
The one big reason to go with the 13" over the 11" for college, is that it has almost twice the battery capacity and I would think that would be important to you. You would most likely not need to even bring a charger with you during the day, while depending on how long you are using it, that might not be the case with the 11". If you had to bring the charger and 11", vs. just the 13", then the 13" is actually more portable to carry.