Actually, your question hits the nail on the head - because you ask two different ones.
The first one is 'do smaller / Matrix-based schools teach magical theory?' The answer there is going to be 'yes' - but that's as far as it goes, because you simply can't do (or study) magic via the Matrix.
The second question therefore is the more practical one: 'are (there) smaller schools to learn how to be a mage?' Any college beyond a basic size worth its tuition is going to have a thaumaturgical arts (or thaumaturgical sciences) program; the type of program may depend on the type of school. A liberal arts university such as, oh, UC-Berkeley (which should have been the first one to have a Th.D. program, NOT UCLA) is going to have a Th.D via 'thaumaturgical arts', i.e. B.A., M.A., Th.D. A 'hard sciences' university like MIT&T, CalTech, or Purdue is going to have their Th.D via a scientific program, B.S., M.S., Th.D. You are more likely to find a mentor-spirit-follower at UC-Berkeley and a straight-up thaumaturgist at the others.
"But hey, Wyrm, those are all pretty darn big schools. How about, say, the University of Wisconsin at Stevens Point?" My theory is that if it's got a student population over five hundred or so, it's going to at least have some of the classes, because magic is of interest to non-mages too. Is it going to have a program? Maybe, maybe not - with the 'active under-control magic' population running at 0.25%, you do have a certain amount of interest in having at least the baseline Bachelor's programs in minor schools, because for every million people, you have 2500 people who are magically active, aware that they are, and sane enough to control it - and for a program, all you really need is a dozen or so every couple or three years. Add in those theoretical thaumaturgists who haven't a lick of magic but can think about it really well, and you have a decent reason for a smaller school to at least have the program as an option from year to year.
But you're still not gonna be able to get a degree in anything but magic theory via the Matrix. Doesn't mean you can't learn that way - after all, MagickNet exists, as do electronic spell formulae. But University of Phoenix isn't going to give you a degree you can bring to the licensing board to become a practicing mage from purely Matrix classes. Real magic requires in-person interaction.