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The money comes from us, the taxpayers (in Canada anyway), and the students' tuition fees.
Scientists have to be careful accepting money from companies as it could be a conflict of interest.
I worked at a US university for 12 years, I can't speak to what happens in Canada, but here in the US it's definitely a mix. Student tuition is not used for research at all, at least not in any research program I've ever heard of.
In fact, research grants are garnished (usually to the tune of 30% or more) to pay general university expenses, and student instruction is part of that budget.
Thanks for the info. I suspect the same thing happens with Canadian universities. Almost all levels of government help fund them and would probably deduct research grants and patent fees from funding.
Here in California the big research schools make a LOT of money by licensing to private industry. There are often a number of prominent law suits over research patents with the universities and private industry. The universities very much want to keep their patents and make money from them.
Looking at the news for CRISPR tells ya a lot about how modern research works and how universities make money.