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.