Pros
Being a non-profit, there's great retirement benefits and "soft" benefits like lots of paid time off, etc., plus really ridiculous things money is wasted on like a game room, "retreats" and trips for an inner circle, etc.
Cons
Unbelievably dysfunctional management. Cronyism and nepotism at its worst. A true case of "the emperor has no clothes" (especially in regard to IT), but if you say anything of the sort, prepare to be screamed at, debased, ignored, and generally made "persona non-grata". Add to that the pervasive "We're a non-profit, so we can't pay competitive salaries and try to make up for it in benefits" leads to a critical mass of sub-standard talent not getting much done at all in terms of the business operational infrastructure.