I drive a manual transmission New Beetle in Los Angeles, and a diesel to boot, so I sometimes get honked at by the person behind me when I don't pull away as fast as other vehicles at lights and hill starts. I'm thinking of getting a bumper sticker made that says "I'm not hesitating, just changing gear"
Hmmm, in Europe, where most of us drive manuals this isn't a problem. It's impossible to tell who drives which kind of transmission from how fast they set off (they only way to tell is whether they have their brake lights on to stop automatic creep on a flat road when stationary). So might this be user error? You shouldn't be sitting in neutral waiting for a green light, you should be in first, with the clutch down the second you see amber, if not before (you can easily judge where you are in a 'traffic light cycle' by paying attention, in my opinion...
Now - I mostly have my foot ont he brake in the flattest of streets, at least for shorter stops - and for longer stops (I know how long red light or train crossing) I switch off the engine. You cant judge on the light.
I also get into a higher gear very early. The motor is unbelievable inefficient in first gear. Thats why it says "the first gear is just for getting moving". If you move more then two length of your car in the first you are making something wrong.
But to the basic problem: Ignore the honking. Its the idiots fault if they cant stand half a single second to wait. They could always switch to another method of transportation if they dont like the experience of car driving.
Not other people make us angry. We decide to get angry on other people. Or not.
Ah, do you know this joke?
The shortest daily used time is the New York Second, defined as the time between the traffic light changing to green and the cab beyond you honking.