Pros
Depending on the department, working in this company challenges you to be resourceful and initiative. On good days, working in this company is very satisfying, especially when you are looking for developing your skill-set as a starter.
Cons
The politic in the office and the nature of the company as a non-profit may limit your chance to grow further in your career. At some point, your routine can be quite mundane and with no further room to grow you might be forced to find an alternative eventually.