It was not always personal; sometimes it was all random. And by 'it,' River meant everything. She was too smart not to know that, but also too smart not to find her loss of power suspect. Many had found her a threat in the past, why not the City?
And she did believe that it was possible the City just wanted a reaction. A rise.
It made her very angry, but she thought that was a good theory.
"It'll mean they can't lock me up," she said. Her eyes went from her plate and the end of the eggs to Hannibal's face. "I can't be put in Arkham anymore."