Bad stories will happen. You could be Mother Theresa and still get bad press.
There are different types of bad stories. Each requires a different type of response.
1) When a story is bad and untrue
If the story is bad because the information is flat-out wrong, that needs to be corrected.
Mainstream newspapers, TV and radio stations will run a correction. The key is to reach out quickly and professionally for that correction to happen. Bad stories happen on A1. Corrections run on A5.
2) When a story is bad but true
If the story is bad and true, you need to control the damage.
The worst types of stories are cover-ups. The cover-up is worse than the crime, with a steady drip of new stories, day after day, as the cover-up unravels. Which it always does.
The best way to respond to these kinds of stories is to rip off the Band-Aid and get it over with. Be honest and forthright and put out the correct information.
Another type of story that's bad and true is a mistake or a tragedy. Always look forward. Don't spend time and energy assigning blame or making excuses. Bad things happen. People screw up. The question isn't whether you can be perfect. The question is, how will you make sure it doesn't happen again?
3) Negative opinions
If the story is a matter of opinion -- your book/movie/CD is horrible, you shouldn't be elected dogcatcher, you're a no-talent hack, whatever -- ask yourself whether climbing into the pig pen and wrestling in the muck is worth it.
This will typically be an amateur using a blog, a call to a radio talk show or letter to the editor. Usually, it's not worth rolling around in the muck.
4) Bad press from a professional critic
When the story is a matter of opinion from a professional critic -- a book reviewer for a newspaper, a movie critic, a music writer or a sports columnist -- there's no point in trying to debate their point of view. It comes across as defensive.
I'd argue for doing the opposite. Reach out and thank them for the review. Agree with any points that you think are right. Don't talk about things they said that you disagree with. Say that you're constantly trying to improve and criticism is part of the business.
You'll be setting yourself up for better reviews in the future. There will be other books, movies, albums or baseballs games. You'll get reviewed again, by this same person. And if you're decent about it, instead of whiny and defensive, and honestly work on whatever faults they identified, that will be rare and impressive.