Plot in Candide
In this case, the King of the Bulgarians pardons Candide not for his wisdom, as a student of metaphysics, but for his ignorance, as an innocent youth incapable of understanding the depths of the philosophy he claims to espouse. Thus, we see Voltaire's contempt for the philosophers of the Enlightenment, who were viewed somewhat critically at that time.
In all likelihood, Pangloss understood that he was being persecuted by the Inquisition for his beliefs. Candide, however, as a young man unfamiliar with the Inquisition, doesn't understand anything that has happened. It should also be noted that this wasn't the usual format of the Inquisition, and that one's crimes or heretical beliefs were almost always made public so that one could be made an example of by the Church. Voltaire sidesteps this to enhance the absurdity of the situation.