What is the ruling on honoring one's parents if the father tells his son that the Prophetic Sunnah and the entire religion are all lies, that mosques raise backward people, and that he does not like to hear the Qur'an?

Denying religion or the Sunnah, and mocking religion and those who frequent mosques, expels a person from the faith. Honoring one's parents is obligatory even if they are disbelievers, so you must honor your apostate father and advise him with wisdom and gentleness, reminding him of the danger of apostasy and eternal damnation in Hellfire, and the danger of mocking religion.