Because as much as it is true that funding influences how some projects get started in academia, professors <i>do</i> get tenure.  And they can and do things which would be totally offensive to a corporate parent.  There is a totally different kind of publication coming out of even the old research labs and an academic institution, much less a modern corporation.  A typical research lab does not need to worry about a bottom line - which a company (like YC) is obligated to care about.