I think there are two strains to the charge of "Jewish supremacy": the first comes from a reversal of power structures (more common on the right, but visible in all radical spaces) and the second comes from an unclarity of categories (more common on the left)
In the first, conspiracy theorists place the blame for their ills (societal or personal) on the Jews whom they hate, oppress, and/or disadvantage, much the same way a parent will blame their child for the abuse they're "forced" to dish out. Accusing a minority of causing all your problems ablates responsibility, giving some power back to the individual, and doing it to such a small minority ensures they can never really fight back. The problem is, when you start to say it enough you actually start to believe it, hence the accusations of Jewish "power" and "supremacy", which are really just projections
In the second, Jews are accused of wielding the power to create divisions, a power which is only used by the majority (read: oppressors). Whereas other distinctions are "real", the line between Jew and non-Jew is invented. This is proven by either the Jews' assimilation into the "real" groups, or the precedence of those groups in a worldview in which Jews aren't a factor. The Jews' forceful (and undeserved) uniqueness creates a new axis on which all previous "real" categories must be reevaluated and challenges the very idea of the categories themselves, hence the charges of Jewish "power" and "supremacy", which are really just bad philosophy