I think you'll find the protest was dismissed as the driver of the favourite had a hand in the tyre being punctured, IMO he crossed the eventual winner a little hastily which brought about the contact. So IMO the margin was not the factor for dismissal rather how contact came about that led to the punctured tyre.

The rules for protest allow for anyone connected with the alleged sufferer to lodge a protest so it may not have come from the driver OR the stewards.