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.

I worked for one. Long hours. Pay was probably below average. It was fun, though. Did it for one season in my youth because the opportunity was good for my resume.

Fucking tough.

I hated my experience at my last job at a non profit.