Supremacists argued for separate but equal. That was the concept that things could be separate but equally good. The Supreme Court answered the question in the negative. That is, things are necessarily unequal simply because they are separate. In order for things to be truly equal, all groups have to have access to the same thing.
As soon as we are divided, separated, it is far too easy for one party to claim supremacy over the other. In fact, that is the only reason for the divide in the first place, so that one part can feel superior to the other part. Look at Apartheid, or the racial divides in the U.S. These things only occur due to separation and superiority.
There is much to recommend separatism over supremacism. Separatism is a racial “live and let live” philosophy. Separatism seems more moral and more just because it is fair to all races. Under separatism, all races get an equal chance to create the forms of life that express their distinct biological and spiritual natures, free from the interference of other races. Separatism is classical liberalism applied to races rather than to individuals. Liberalism is, of course, the “common sense” of American culture, which goes a long way to explaining the appeal of racial separatism. Supremacism is, by contrast, deeply illiberal in spirit. The supremacist wants his own race to have its own homeland(s) where it is free to control its own destiny. But he would deny the same freedom to other races. He wants his own race to rule over others. This hegemony need not be exploitative. It can be benign, even paternalistic and benevolent. But whatever form it takes, racial supremacism denies that all races have equal rights to self-determination.
There is no difference between Separatism and Supremacy. On paper it could be made to seem different, but as we have learned from history, eparate will be inherently unequal and naturally become Supremacy. We saw this in America in the Jim Crow days. And common sense will tell you that when people are separated they will have different resources and a disparity is inevitable. What is the point of being separate if the ultimate goal is not some form of supremacy? One may be ignorant to how the story will end, but the best of intentions can not alter the outcome.