Pros
The people who work there are great, real sense of camaraderie. Your colleagues (in ops, flight ops and crewing at least) will stick by you in the difficult times and help you out. Excellent experience that you can take elsewhere after you've been there a while. The staff work hard to make it a good airline despite its problems, so that's a good morale-boost in a way.
Cons
LOTS of disruption to the flying schedule so the ops & crewing department is very busy and stressful. I don't think it would be anywhere near as bad in other departments e.g. HR, IT, revenue and accounts etc. Poor pay compared to other airlines, and you have a lot more responsibilities as the team is small (although that could be an advantage as you get experience in lots of areas). Not much formal training.