Personally, I would never capitalize apartheid. Deliberately, in order to emphasize the despise for this indisputably wrong idea. Contrary to what dictionaries advise, I would do exactly the same for nazism or stalinizm, unless somehow any of them is used in a clearly positive context (which I cannot really imagine). But this is my personal approach.
EDIT: ActuallyAs for facts, there seems to be quite a lot of contradictionI guess people confuse two things. Cambridge online dictionary says 'Nazism', but at the same time there's 'apartheid'. My conclusion would be that 'Nazism' was the official doctrine of the German state, while 'apartheid' was not in the case of the RSA (though it existed there in practice as part of the social system). In Germany, there was National Socialism (Nationalsozialismus), the National Socialist German Workers' Party (Nationalsozialistische Deutsche Arbeiterpartei or NSDAP), consequently there was Nazi Germany and Nazism. As far as I know, the term apartheid was never used in such a way. It's just a common term to describe the social system of racial segregation in the RSA (Afrikaans for "separateness", or "the state of being apart"). It's a concept, so no capitalization by rule.