To some people it doesn't.
This is where you fall down, logically - and not infrequently.
YOU believe that the Confederate flag (and it's not really the Confederate flag, but that's beside the point) represents racism. To you it does. There's nothing wrong with that. But to many people, it doesn't represent anything of the sort. Thusly, for you to argue right vs. wrong with respect to people's beliefs and how they feel is just silly.
As to the topic at hand, you clearly don't understand the nuance and complexities of modern corporate compensation structures, since drawing a distinction between "bonus" and "variable compensation" is not "semantics". You're wrong. And you haven't admitted it. So...
The other side of the argument is that while I agree that the Flag may represent something else to some people(pride of being southern) or what ever- they also know that it is offensive to most and fully understand that most DO consider it racist. So, hanging on to it now does switch from their non-racist reasoning to being racist.