There's a tradition in England - I don't know how old - of abusing red-headed people. It's a genuine prejudice in England. From this facebook page:
'Ginger' in England basically is like saying:
"Look there's an ugly, smelly, no friends, socially unacceptable, negative, aggressive, angry, violent, unclean, nasty, non boyfriend material, low self esteem, unattractive, social misfit, nerdy, moron, low education, non human...etc etc etc"
The term 'ginger' didn't become 'mainstream' just because of that South Park episode, I was being shot at, having acid thrown over me, stabbed, headbutted, punched, spat on, kicked, dehumanised, singled out, socially excluded, avoided, belittled, character assassinated etc since I can remember and to be fair I found that treatment was at its peak years before that South Park episode was even thought up.
This spread to the US in 2005, when Cartman tried to incite violence against redheads in a South Park episode with "Kick a Ginger Day".
What's interesting is how this meme is spreading in the US: As humor. This meme is promoted by sites like CollegeHumor.com and MyLifeIsAverage.com, which mine it as a source of ironic humor. The Cheezburger Network is pushing ginger-hatred almost as aggressively as they push pedophilia as a fount of humor.
Are humans capable of, collectively, keeping real and humorous/ironic racism separate? No, they are not. What South Park "kicked" off as an ironic commentary on racism is becoming actual racism.
One clue that you're going too far in your ironic humor is when you start finding the real thing funny.
Do humans have an instinctive need to bond over shared prejudices? Is combating racism a game of whack-a-mole, in which society invents new prejudices to replace the ones being taken away?
I think the reason that it's considered funny is that, while many consider racists stupid, it is almost unbelievably silly to think of someone as sub-human because of their hair color. It is true that I haven't actually experienced prejudice of this kind but many of my red-haired friends routinely make ginger related jokes. At least in my circles, racism against red-haired people is entirely ironic.
It might be worth noting that we were first exposed to anti-ginger feelings though humor, not from any legitimately racist source.
I can see strategic reasons for that belief-- make a behavior low-status in order to discourage it--- but there's a problem that it's false. There have been intelligent racists and high status racists, and I think the belief that racist is especially the province of the poor, stupid, and ill-educated has led to 'racist' being a much more explosive insult than it needs to be.