Hi coreytothecup.
You bring up a great point. And I think many people do see bad things as being for the ultimate good and/or a kappara, but they dont express hakaros hatov.
Maybe that is something we should start doing, unless it makes us come across in an undignified way, or like a masochist, like in the example you gave of someone getting hit responding to their assailant with, “Thank you, I really appreciate that.” Or, “Can you hit me again, just for good measure?”
While what you say is totally true, how would it come out in the wash if people really acted on it?
“Thank you for robbing my belongings.”
“Thank you for terminating my employment.”
“Thank you for ripping me off on this repair bill.”
Again, while everything is certainly for the ultimate good, openly showing appreciation on every level can make us look strange.
I am sure other posters will have interesting perspectives to share.