How do we know it applied to all of them?
Because it was a system of racial oppression that worked in exactly those terms. Obviously. The exact severity of the impact on any particular member of the victim class varies, but the premise that they didn't all suffer systemic harm from it is preposterous - tells us only that you're either ignorant or disingenous.
There are wealthy minorities who live pampered lifestyles of privilege in all countries. I bet you anything that the majority of black med school graduates in the USA had a comparable upbringing to white med school graduates. They come from professional families in posh homes located in expensive white collar areas. I'm sure that the same holds true for some blacks in South Africa.
In the first place you are making a serious mistake by projecting your perspective on US society on South Africa. Apartheid was qualitatively worse than Jim Crow, and persisted until a lot more recently. The level of racial inequality that persists in South Africa is severe - you've never seen anything like it in the USA. We're talking shanty towns with open-ditch latrines, no running water, and no electricity, right next to modern resort towns. It's staggering, and points up what a fundamental error it is for your (and adoucette, etc.) to project your agenda for American race relations uncritically onto South Africa. If you aren't going to understand the relevant situation in an honest way, then at least spare us the cheap attempts to pretend you don't need to do so.
In the second place, it is always the case everywhere that the applicant pools for post-graduate education are going to be disproportionately from the more successful demographics. Nevertheless, the racial disparity remains obvious in the applicant pool - there being fewer rich black South Africans than white, and them being less rich than the whites - so one can scarsely argue that there isn't a visible disparate impact to be addressed there. Likewise, addressing the impact at that particular level is very important to addressing it more generally, even if the individuals being given a boost aren't the worst-suffering ones. You train more black doctors, and you end up with more wealthy, stable black families, better medical service in the black communities, etc. It has a huge carry-on effect, which is one reason that these programs are used.
That said, I'm open to the suggestion that the post-graduate level is not the most important place to address the problems. Addressing basic literacy, primary education, high school, medical services, job opportunities, etc. are all also very important. But in the first place we don't have to choose one or the other - all aspects can be addressed simultaneously, and post-graduate stuff is important. And in the second place, fixing things like primary education is very expensive. You have to come up with a bunch of extra tax revenue to pay for it. Affirmative action is cheap - you don't pay any extra out of pocket, you just rearrange who gets admitted to which school. So, it ends up politically more tractable, since you don't have to ask anyone to pay more taxes, and moreover most of the electorate won't be personally affected anyway.
An interesting point: a broad-based tax hike to improve primary education and services amongst disadvantaged groups would seem to be exactly what you and adoucette are calling for. It doesn't discriminate against any particular individual, the benefits are broadly distributed, there are no hand-outs to people already successful enough to pursue med school, etc. And yet, there seems to be no support for such. Rather the opposite - people would rather move away to avoid having to pay into the school systems to serve minorities, etc. So this looks like so much craven pretense. If I seriously thought that you guys were arguing for having everyone pay, and using the money to fix up schools and social services for oppressed groups, then I could take these supposedly-principled objections to affirmative action seriously. But I don't see any of that. All I see is a rush to find any excuse to both oppose addressing inequality and also construct a pretense to avoid admitting to racism.
By assuming that the black med school applicants of South Africa all suffered from racial victimization, we are generalizing and that usually isn't an admirable thing to do.
By pretending otherwise - in the face of already-visible data establishing exactly such - you are arguing from willful ignorance, which is an outright dishonest, disrespectful thing to do.
Even if just a few of those applicants are benefiting from admission policies designed to reverse racial oppression when they weren't actually hurt by it, then the policy is flawed and unfair. The integrity of the admission process becomes questionable at that point.
A few perverse exceptions to the rule are just that. You're seriously going to argue, with a straight face, that the mere possibility of some hypothetical student who didn't suffer
too much from Apartheid might get an unearned break, means that reasonable, effective measures to address a huge problem with inequality are unjust?
Again, it's just transparently racist: millions of systematically oppressed blacks are held to be less important than a single wealthy white person not getting into their first choice of medical schools. To even advance such a premise with a straight face requires one to be so steeped in white supremacism as to call any pretense of principled concern into serious question.
It also has the effect of making it appear as though minority races can't compete on their own, which isn't a positive image.
Getting rid of affirmative action would skew the med school student bodies drastically towards white people, thereby providing equal grounds to claim that blacks can't compete on their own, at least to those audiences who are so glaringly racist and/or ignorant as to ignore the obviously relevant history. Which audiences we shouldn't be catering to regardless, but it remains that no difference would be made there. Whether racists claim that blacks are inferior because they couldn't get into med school, or because they needed help to get into med school, doesn't matter. Reasonable people are not going to look past the obvious history to construct justifications for racial supremacism either way, and those are the only people worth catering to.
Also, black people in South Africa are not a "minority race." That would be the white South Africans, who apparently needed to maintain a vicious system of racial oppression to prevent the other races from competing fairly with them. Not a very positive image, is it? Or doesn't your racist "reasoning" apply to white people?