It's probably a number of things. Your own article said that enrollment was down even before the protests, because neighboring Illinois had dropped its own in-state tuition.
The protests brought to the forefront a number of issues with the school (some related to diversity, some not), which likely made it less appealing to the out-of-state students who've stopped enrolling. As I've posted numerous times, a LOT of people were unhappy with the administration for a number of reasons.