Whoopi’s confusion is understandable IMO. The modern West has tended to impose distinct categories of identity - “religion”, “race”, “nationality”, etc. - on everyone, categories which would have different implications or make little sense in terms of pre-modern identities (and in the specifically American context it seems to me that rather clear-cut racial distinctions tend to be foremost in peoples’ minds, for obvious enough reasons). Given that Jewish identity derives so much from a rich pre-modern Jewish heritage, with all its complexities, it tends to defy this modern categorization, leading in turn to misunderstandings such as this one.
In any case she apologized and that should be the end of it.