Non-magic people (more commonly known as Muggles) were particularly afraid of magic in medieval times, but not very good at recognizing it. On the rare occasion that they did catch a real witch or wizard, burning had no effect whatsoever. The witch or wizard would perform a basic Flame-Freezing Charm and then pretend to shriek with pain while enjoying a gentle, tickling sensation. Indeed, Wendelin the Weird enjoyed being burned so much that she allowed herself to be caught no less than forty-seven times in various disguises.
So muggles hated magic users but didn't have the ability to persecute them. Meaning Salazar had no real reason to hate them. However one might say their willingness to persecute them is enough of a reason.
