"The only time university endowments pay taxes is when they invest in debt-financed financial firms such as private equity funds and hedge funds. These investments are considered a business activity unrelated to their tax-exempt missions."
Somehow that part of the article didn't click for me. The NYT article linked in the following sentence does a great job of explaining why they are being taxed if you don't have a finance background.
In addition to the sibling comment there’s also been some disclosures regarding investments in industries that could plausibly get universities bad press — such as coal mines.
Given the current cost of coal relative to renewable sources that seems like the exact sort of poor investment that the public or interested parties should know about so it can be rectified.