Cain refused to acknowledge or cooperate with the government she claimed to serve. When the Pegasus found the Rag-Tag Fleet, Cain once again was under the authority of the President of the Colonies and the Admiral of the Fleet. Cain refused to accept this authority. Her actions proved to be the actions of a rogue military commander bent on a personal vendetta against the Cylons.
Well actually she kind of was the Admiral of the Fleet at that point, that was the problem form the military stand point the nutcase outranked Adama so he kind of had to follow her orders for the most part.
Which was probably the other reason besides having two Battlestars that Adama got promoted at the end of the arc just in case they ran into another insane admiral Adama could pull rank and cut that stuff off before it starts.
Though you're right about the refusing to except the president's authority.