I doubt present-day Wizarding prejudice has much to do with the ideals of the Founders. I think if was nicolthewhore who suggested that the basilisk, the forest, the squid, the maze-like quality of the castle were all originally protections. And as we're talking (lord, when was Hogwarts founded? *consults HPL*) c. 1000 CE... Well, witch hunts were centuries away, Wizards freely intermingled with muggles, lived with them, married them, etc (meaning that you actually had far fewer pureblood families, the vast majority halfbloods) - the Norman Conquest might not have even happened yet - everyone and their brother was at war... Hogwarts was in all likelihood a fortress, and Slytherin might have feared enemy invasion not just in the form of Muggleborns but in the instance of anyone of dubious political affiliation.

*insert more poor paraphrasing from Red Hen*

bah. i am tired. everyone just read everything Red Hen has to say, then pretend i did a better job of copping some of their arguments, whatever's relevant to this discussion.