I speak as if it is the only kind that has the INTENT of creating a chilling effect.
But that isn't the only kind, organized crime will often try to dissuade competition and create warnings to rivals and send messages with violence. I'm not really sure what I think of that part of it, but I do know that crimes where the action actively intends to send a message should be punished more than crimes with action and no intended message. We as a society have the ability to make laws to try to form a future society in an image we want.
I want a society where there are no people who have thoughts or beliefs which would be considered "hateful", as in racism, sexism, homophobia, etc. By punishing those more harshly I believe it adds momentum toward reaching that destination.