Father Sebastio's feelings towards Blackthorne are very clear from the first time that they meet. Blackthorne has just been brought back from his ship and Sebastio is waiting on the shore. His first words of any substance to Blackthorne are "I'm Father Sebastio and you are a heretic Dutchman pirate." Soon after that, he tells Blackthorne that he and his crew will be killed and Sebastio wishes that God will burn them "in hellfire for all eternity."
The reason for this hatred is that Sebastio is Portuguese and Catholic. He believes that Blackthorne is Dutch (because he came on a Dutch ship) and Protestant (which he is). This was a time of real hatred between Catholics and Protestants, which is the major reason for Sebastio's attitude towards Blackthorne.