Dune is obviously inspired by Islam. Even in the books they refer to the Fremen war as "jihad". In later books memories of the early Fremen are of being Bedouin Muslims. I don't think Herbert was trying to deny it in the books. It's literally spelled out in the text that the original Fremen were Bedouins.

If he downplayed it in interviews it's likely to avoid being cancelled by conservative Christian media.