Jesus told the story of Jonah to make a point in the Gospel of Matthew and Luke. Matthew 12:40 Just as Jonah was in the belly of the whale three days and three nights, so will the Son of Man be in the heart of the earth three days and three nights.
If the story of Jonah was a "fairytale" as some would have us believe, then when Jesus uses the comparison it would have been like Jesus was using a fairytale to prove the validity of what He was saying. It would make no sense!
Jesus would be saying; "Just as Jonah was in the belly of the whale for 3 days, which we know is a myth, so the Son of man will be in the earth for 3 days!" For more, see The Catholic Encyclopedia online, New Advent: Jonah.