Huh. I was also disturbed by it, and in general I appreciate better movies which offer something more positive. However, I did think it was thought-provoking and interesting, and worthwhile for these.

Obviously, her fantasies were dark. And the faun was clearly the mirror image of her fascist stepfather, and was drawing her into evil. (I saw the mandrake root as potentially dangerous but not poisonous. Within folklore, it is said to aid female fertility, but if it is taken out of the ground in the wrong way, it screams and all those who hear its scream die.)

To me the point of the movie was that mixing of fantasy and reality. The lure of being the elite, and of helping her mother, drew Ofelia to almost want to work with what was obviously dark and evil. The fascists were the blatant evil, but the fantasy let her almost think that the dark stuff was somehow OK. I didn't think the message of the film is against fantasy, but it is cautionary that it can lead one into evil. Ofelia almost came to hating her evil stepfather so much that she would kill her baby half-brother in revenge. She resisted in the end, but I feel that she would have done better to not kidnap him at all but instead run away.