... THE STUDENTS ARE ALREADY PAYING FOR USE OF THESE RESOURCES ...
Most students are not. Most of these inventions were produced by graduate students performing research. Most graduate students doing research in areas that have commercially valuable applications are paid to do that research.
So almost all of these patents and royalties are coming from the work of graduate students who were supported by research grants - employees of the university, essentially.
I'm a graduate student in computer science. I'm paid to do research. Honestly, I'm not even sure whether I am allowed to use the code I've written here after I graduate. But I can release it with an open license (at least open for research use) before I leave to get around that, I think. It's a fairly murky area, and I get the feeling most grad students don't understand the full implications. Most times, no one really cares. However, it is very clear that if there is money involved, the university gets a cut.