The problem is not that the topics themselves are toxic, but that only one point of view is identified as such. I only mention these "flamebait" topics as examples, not to discuss them or choose a side.
Gamergate
Gender Equality/Equity
Affirmative Action
White Privilege
The various subjects in James Damore's recent memo [note, he was fired for honest, sourced feedback that was explicitly requested of him]
Politics in general (especially anything remotely pro-Trump or pro-Republican)
If you pay attention to dynamics on reddit, for example, certain sides tend to be stifled, regardless of any potential merits. I am not choosing sides, just offering examples where certain opinions are immediately identified by communities as toxic, and no discussion is even attempted.
Hell, there is a growing movement among feminists, at least a vocal minority online, which claims that our modern concept of masculinity is "toxic."
The very word is turning into a catch all for "opinions I don't like," which seems to happen any time one attempts to censor information.
Finally, consider this: if the topics I've brought up are so clearly, as you claimed, not merely "differences in opinion," then why do they attract such heated discussions, with contributors on both sides, even on HN?