I...actually don't. Sure, taking all the shortcuts means that there's the more-than-occasional pedestrian homicide, and I sometimes beat up people when they're in my way or give me some bad lines, but that's pretty much it*. This isn't me being a moral knight or something...it's more that I see it as a waste of ammunition to shoot at groups of bystanders. I never understood the "fun" there is in murdering innocents. Oh, and of course I do objectives that require it if needed (like the mayhem or rampage missions), but those usually bore me.
*Okay, and the mascots in Saints row. But those actually ASK for it.