Part of that is a deliberate strategy on the part of some universities, based on a guess that they'll get more in donations from corporations, spinoffs, and successful alumni voluntarily, than they would get by being tight-fisted with IP. Plus, it increases the university's prestige to have their stuff involved in more products, and their alumni involved in more successful ventures, so there's a cost to doing anything that would complicate stuff up-front. The goal is to get it on the back-end instead: don't hassle the not-yet-successful startup, but if they IPO, nag to see if they're willing to kick in a $50m building or write you into their will.

I'm not sure which version of the calculus is right, but it's at least plausible to me that universities stand to lose more in donations/prestige than they'd gain in royalties if they took stricter approaches to patent licensing.