As bdcravens says, what upsets some is that THIS executive and THIS situation was deemed worthy of sweeping under the rug, paying out the $90m and giving a hero's send-off of sorts (yes, anyone with eyes knew Andy was forced out, but there wasn't any chatter that I was aware of that he was forced out for personnel reasons. Instead, it was assumed to be a power struggle that he lost.), when many others are often let-go for far less compelling reasons (there might not be an HR report that finds fault), without their options fully vested.
It isn't clear if Rubin's actions reached a level that would breach his contracts morality clause (assuming one existed -- and one almost always exists), which would allow them to fire him with cause -- but the fact that an internal investigation found that he acted inappropriately, would at least indicate there was a legal way to fire Rubin without paying him $90m.
(I am not a lawyer, FWIW.)
My gut tells me that at the time of his ouster, Alphabet was worried more about the optics of a protracted lawsuit with Rubin, rather than a cover-up for a harassment claim coming to light. Presumably the other individual in the harassment case settled and signed an NDA, which would preclude public discussion and disclosure.
In retrospect, that was a bad call -- because in 2018, the optics of sweeping credible harassment allegations by a senior executive under the rug and then guiding them out the door with a $90m settlement is something that sickens and angers many individuals.
It's the sort of move that is incredibly common in other parts of business (Hollywood and the media business in general), but that doesn't make it OK. And it is particularly offensive when the industry in which it takes place -- and the company it is taking place at -- have a history of trying to be "better" than the status quo.