Maybe this doesn't apply to all situations. It's just that in my case, especially in music technology, I often see funding being allocated to things that I think are somewhat disappointing, and of course, that's just my subjective opinion. More often than not, it is an overall lack of funds. Many open source projects are actually of great academic value and worthy of study. In fact, many contributors to open source projects love blogging. I often feel more rewarded reading these blogs than dozens of pages of academic papers. I can clearly feel that I will have more time to make pure open source contributions during my funded Ph.D., or even when I am lecturing at the university. But now I have to balance it with some practical considerations.
I do think a similar thing to the GP, on my case it's because universities have the problem of "how to fund potentially society-changing projects that mostly go nowhere and depend on really qualified people" closest to solved than any other institution.
There's a lot of problems that I do think universities could be working on. Creating free software is one of them.