Time, time, time and patience. If possible, try handfeeding (or just holding his dish) for his meals, so that YOU are the source of the good food, and therefore your presence is a good thing. Spend hours grooming, and talking to him. You can even sing him songs – just get him to look forward to your being there, and he may come around. I don’t care for your trainer’s response at all. If he is in charge of things, it was his responsibility to ensure that the horse would be safe for anyone to handle, and he’s had three years in which to do it. He may also be aggressive because he is in a stall for too long. Horses should be outside as much as possible.
It is never the horse's fault