I would not recommend it for a 3yo. Even a four year old would have trouble understanding the story line and for a 3yo would go over head! Can you see Madagascar 3 instead? I had doubts for my 10yo to see it until I saw the reviews. It is rated PG and does have scary scenes.
My 4 year old and 6 year old were fine in it, but it does have what they call the bogey man (pitch black). So for a sensitive child it could be quite scary with the dreams being turned to nightmares with scary horses and so on.