To try and let your horse know you won't hurt her/him, use approach and retreat.
Run your hand slowly but steadily up her neck until you reach a spot she isn't sure about. (let's say it was the back of her ears.)
Take a brush or you hand (anything really) and brush from her withers and work your way up. When you reach close to her ears, brush by that sensitive spot very quickly and go back to brushing the middle of her neck. Do that a few times until she thinks it's ok. Then once you can touch her ears without too much movement, take your hand and so the same thing with places on her face until she is OK with it all.
It will take lots of time, but do it right and stop on a good note the first time and she will be better the next day.