Normally I would agree, but not with head shying. If you keep the pressure on when he gets nervous, you will have to follow his movement with your hands towards his face, which will just reaffirm his thought that hands are "coming at him". That's why I said to move back to less sensitive areas BEFORE he has a chance to get upset.
I agree with usandpets as well. I don't want to move my hands away when he starts to get nervous, as that will reward him for being nervous. And I don't want to not make him nervous at all, because then I'll never get anywhere near his head.
An issue like this is very dependant upon TIMING. You should be pressuring his "comfort zone" a little bit (its the only way to make progress) but you need to be aware that you don't push a little bit too much and make the horse freak. There's a really fine line between those two reactions from the horse, and it takes experience to understand that line.
You also want to keep your entire body "casual". If you are standing three feet away from him and reaching .... that's like a predator. If you are holding the lead rope in a death grip really close to the halter .... that's like a predator. You want your body to convey that this is no big deal, just a run of the mill, and be relaxed. Of course, you do want to stand at the horse's side (not in front of them) for your own safety.
And patience, patience, patience!! Rub/brush his neck and slowly more toward his head. Watch him. The very instant he flares his nose, raises his head, twitches his ears, quits blinking, etc means that he is nervous and you have entered a pressure zone. HOLD. Do not move any farther, but do not back off. The very instant you see any sign of relaxation like licking lips, lowering head, blinking, a "sigh", or anything, move your hand back into a very safe zone to rub him.
You don't need to drill him on it for 45 min a day, but you do need to be very consistent. Work on it for a few minutes every day, on both sides evenly.
I also wouldn't let anyone else handle him but you right now, because you are very aware of his problem and are gonig to be working to fix it. Someone else can come in there and set back your progress.
He's had this issue smoldering for a long time. It'll probably take a long time to fix it and it may never go away completely. But he certainly should be capable of accepting a head touch.