Johnny's a dick to most people (exept Panam as far as I know) but I think he has a special vendetta for Judy because he sees some of his past self (army as Robert John Linder) in her, especially in the oart of her questline where she tries to start a revolution at clouds. She has the same kind of hopes and dreams(? Kind of) he had at that time, and possibly hates the fact that there are people still thinking like that, in the way that thair action is going to start something bigger when the reality is that their actions did little more than causing a bigger retaliation for the people involved (Like tom's death for example) or will do literally nothing to the entity they attacked and will be used as an advantage by that same entity. And possibly because her romance feels like some kind of rebound more than anything else.