Harvard's rolling over was particularly annoying, they have a 52 billion dollar endowment! If any university could afford to make a stand and lose funding over it it's Harvard. What's the point of this massive pile of money if you never dip into it in exceptional circumstances?
Universities typically only spend about 5% of their endowments per year, since it has to last forever. And much of it comes with restrictions on what it can be spent on, those come from the donors wishes. So money in the endowment that's for the theater department or to support an econ professorship can't be repurposed to support federal funds that supported cancer research.
Yeah they try to make them perpetual by only spending less than their growth each year but with 52 billion you could afford to draw down a billion or two (2.6 billion would be 5%) and that would fund research for years.
Harvard's endowment could fund all research at the university for many decades.
Harvard chose to roll over for Trump, and I think the main reason is that the board of the Harvard Corporation largely agrees with him.