In today's interesting fan theory: Knowing of the threat muggles posed to wizards and witches, Salazar Slytherin planned ahead and built a saferoom where the students and staff of Hogwarts could hide. This secret chamber even contained a guard animal to protect them. Getting to the saferoom was something he entrusted only to members of Slytherin, because any other wizard would have muggle relatives, and therefore could be compromised in a crisis situation.
Later, there was a falling out among the founders of Hogwarts, one so bad that even Godric Gryffindor and Salazar Slytherin parted ways, though they had been best of friends previously.
Over the centuries, bigots in Slytherin twisted the legends so that the basilisk in the Chamber of Secrets came to be seen as a plan of Slytherin's to purge the impure and mudblooded from the wizarding community.