Whoopi is an African American woman. Native Germans and the Jews they persecuted would not be seen as different races by the way we define racism in America. It's just a matter of perspective. To Whoopi (and frankly most black people in America), Jews are white, so her point was that the Holocaust wasn't about racism because it was between two groups within the same race.
Now, she's wrong, because Germans didn't see race the way we do. To them, the Jews were another separate and inferior race, and the Holocaust was implemented to destroy that race. So it was most definitely about racism.
What Whoopi said was ignorant, but as usually people are going overboard and lying about what was said. She didn't attack Jews and she didn't downplay the horrors they faced. She just got tripped up on terminology.