Charlie doesn't know much about other types and this type of hallucination did work on a charmeleon, so he figures it could work on Flare as well. You know that guy you meet on the sidewalk who thinks that certain people all behave the same way? Yeah, that guy is Charlie. In case you didn't know yet, he thinks all pokemon of every other type think the same. He is very... uniformed should I say. Don't worry about raising every possibility about what Flare could do. I just write Charlie having only the simplest plans because he thinks that's all he ever needs, and now it's finally bitten him on the butt.