I think that some people are bothered by it a bit because the right is being called nazis/fascists by a certain portion of the left all the time (alt-left I guess). I don't think anyone is bothered by nazi killing because they agree with nazis or think of themselves as one. Back in the 90's and early 2000's, no one was being called nazis so no one cared that nazis were the villains in games. Now, nazi is almost synonymous with asshole or right-leaning with how it's being used.
Personally, I don't care. Nazis are long dead and I know that the vast majority of the right or left aren't comparable to actual nazis.








