I never said she should fear you. What I said was that you should try asserting authority over her, there's a difference.

[She pauses. There's a bit of an edge to her words, but as she continues it vanishes.]

You need to make her realize that you're her trainer, and thus you know what's best for her. A person isn't going to listen to someone they don't respect, neither will an animal or a Pokémon. You can't just "be nice" to these things all the time and expect everything to work out, discipline is a necessity on occasion. A child doesn't get rewarded for punching their parent in the face, after all.