Unfortunately the pilots that do get in trouble usually bring it upon themselves and then blame others for their misfortune. No flight department wants to hear someone whining about how it's everyone else's fault for XXXXXX. Pilots have been let go for doing something stupid, then trying to cover it up/lie about it.

In most cases, if you did something wrong, stupid (bend an airplane, confrontation, etc) are honest and upfront about it, the flight department will go to bat for you in helping you to keep your job.