Pros: workplace culture, benefits
Cons: typical hr antipathy
My work schedule and environment are excellent - very supportive and flexible, with a lot of latitude and trust for me to develop new and better solutions (which produces better results for our projects while improving my skill set, a win for all involved). However, this is all due to my specific manager's style, so I can't generalize to other people's experiences. Generally, though, there seems to be good non-profit university culture: Good work-life balance and a culture of developing employees.
The pay is fine and benefits are very good, with lots of healthcare options at different budgets and choices for retirement savings.
However, I have had problems with claiming benefits from HR to which I was entitled, involving interpretations of vague written policies. Even when I prevailed, implementation was delayed in an almost punitive fashion.