University IP based endeavors tend to be non-software areas where patents are legitimately results of very expensive research endeavors staffed by multiple PhDs, not "using a database engine to store a wish list."

They do resemble patent trolls in that most of their business is licensing, not directly making products. However it is more based on selling: "Hey we have this cool technology, license it!" rather than showing up out of nowhere and extorting settlement.

More that the university gets a cut by licensing patents to the employee inventors, in exchange for incubation support. Not trolling the general business public.

For example, Google paid Stanford something like $1B in exchange for the patents of work developed by Googlers at the university.