The best explanation we can figure is that Peppermint Patty sees a lot of her father in Chuck, she asks this question herself sometimes: "How can I like a guy I can strike out in three straight pitches?"
Marcie likes Charles because of his sensitivity. The interactions she has with Charles frequently involve an acute understanding of Charlie Brown's sensitive side, such as telling him to not force himself to become the mascot for Peppermint Patty's baseball team because she knew it would be degrading, and because she knew that if she didn't intervene, Charles would do nothing at all.
I always thought it was funny/cute how both girls' nicknames reflected how they view Charlie Brown. Peppermint Patty's "Chuck" sounds a lot manlier, like a father. Marcie's "Charles" is more refined in contrast.