I know there have been questions in the past about rep sharing between meta.stackoverflow and Stack Overflow, but I believe these all predate the sharing of rep between the other metas and their parent sites so the existing answers do not address the fact that the current situation is inconsistent.
Today, meta.superuser shares rep with Super User, meta.serverfault shares rep with Server Fault, and I believe a similar rep sharing is in place with all other Stack Exchange sites other than Stack Overflow and meta.stackoverflow.
I could see an argument for not sharing rep between meta sites and their parent sites (though I disagree with all of the arguments of this sort that I've seen). I could also see (and happen to agree with) arguments that metas should share rep with their parents. I can't, however, see any reasonable argument for not sharing rep between meta.stackoverflow and Stack Overflow when all other metas share with their parent site.
Any answer that argues that reps on meta.stackoverflow and Stack Overflow should be split should also give a good reason for them not being split on the other sites. Let me say right now that I do not consider "for historical reasons" to be a good argument for the current inconsistency: recomputing rep for meta.stackoverflow and Stack Overflow users should be pretty easy, and given that it'll only increase everyone's rep on both sites it seems unlikely that anyone would complain about unfairness.