There are a couple different schools of thought on that. If it's a nail or screw puncture (not a gash) within the tread area, sure, I'll repair it. I've plugged several motorcycle tires and countless car tires, and I've never had one fail. And I've never either personally known anyone, or even read about anyone having an accident that was caused by a tire patch or plug failure.
It's a judgment thing I guess. I wouldn't plug a track tire (wouldn't pass tech inspection anyway) but I don't have a problem riding on the street with a plugged tire. Obviously, you can't go wrong by replacing the tire.