According to former FAA Inspector Chris Monteleon, the FAA were in bed with Colgan management. He was tasked to making sure that Colgan was in compliance with Regulations etc. So when Monteleon tried to tell his superiors that Colgan was not in compliance his manager told him and I quote "Mike Colgan is a friend of this office" (I got this from Flying Cheap documentary)

(Note: Mike Colgan was the President of Colgan at the time)

But they are not the only airline that pulls these shenanigans. My guess is that Colgan (Now under different management) thought they could get away with it.