Rainbow Dash is very well aware that Scootaloo is her Number One Fan. That doesn't mean she has to like it. While she enjoys the attention and encouragement she gets from the little filly and her other fans, she isn't too fond of actually dealing with them. It's nothing personal.
But after she overhears Scootaloo being bullied by some of her classmates about her flying ability, Rainbow Dash decides that perhaps it's time her Number One Fan got some encouragement of her own.