We can assume that Cartman's hatred for ginger kids was caused partially by his hatred of Scott Tenorman, who was a ginger. We can trace his desire to execute diabolical plans and operations to "Something You Can Do With Your Finger". And we can even guess that his more recent hatred of Wendy Testaburger started in "Chef Goes Nanners", when she broke his heart.
Yet the origin of his most prevalent and well-known bigotry--Jews--has yet to be revealed. It's likely that a lot of it came from him being annoyed and pissed off by Kyle (and his mom) and building it from there, but his hatred of them was clear from the very beginning; before any of that happened.
So unfortunately; there doesn't yet exist an answer to your question.