My ex-wife worked for non profit for most of our marriage, these are my summations of her frustrations over the years. She and I both were pretty severely depressed during this period as well, so keep that in mind:
- they are run like a business, and can be just as political
- you will be overworked and under paid
- career prospects are limited
- the board is sometimes full of sexist idiots
- you will meet some wonderful people but still sometimes work with and for idiots
All that being said you are doing something that typically is doing good for humanity.