Although I don't like the racket, I think honking is a GOOD thing for one simple reason -- it helps you train your reflexes for when you really need them.
You do not want to jump out of your skin when some jackass buzzes you and lays on the horn. For one thing, that's exactly what they want so they'll keep doing it. More importantly, you're far more likely to crash (and less likely to make a good decision) if your nerves let go.
In emergency situations, you only get one shot and it's really important not to screw up. I tell my wife and my friends not to honk at other cyclists, but that they should honk at me and not give me much clearance. I'd much rather have people who care what happens to me help me train my reflexes rather than only work with those who hate me or are dangerously stupid.
I think being accustomed to being honked at and buzzed greatly enhances my safety. On the extremely rare occasions when I encounter a hostile motorist, I tend to regard them like a spoiled 5 year old -- I'm a bit disgusted, but I basically ignore them. I've also found that during these encounters, I tend to remember to do things like watch for other threats and evaluate evasive maneuvers (last year I had to leave the road to avoid getting hit by a car that lost control on the highway).
It's hard to do the right thing if you can't think because you're terrified. I say let motorists honk and get over the discomfort.