Why Doom works with Red Skull
...same reason why it was okay for Magneto to be retconned as a Gypsy Villain at one point when a Jewish Villain was seen as scandalous.
Racism affects people differently in different places in different circumstances*, and currently, while there are definitely still people who are racist against Jews, that tend to be more condemned then negative portrayals of smaller minority groups.
* Personal Example: There has been at least three old white dudes who assumed that by being friendly and respectful and ASIAN, I'm For Sale, but at the same time, I have the dubious comfort of knowing that if I go missing, the news in Toronto would be all over it, the way it wouldn't if in the case of a missing black woman (and many has indeed fallen through the cracks). Back when I had short hair, and was mistaken as a boy 50% of the time (and therefore, does not get the Girls Are Non-Threatening Exception), I notice that a classmate of mine who was black always get suspicious looks when we walk together, just him, even though he's actually very stereotypically girlish, I've seen new teachers look at him like he's going to pull out a knife or something.