I would say that if the tractor is in the pasture it needs to be moved. I have seen horses left out with pick up trucks in the pasture with horrible results. The horse ran towards the barn and hit the tail gate, the horse opened its knee joint and had to be euthanized. Horses pastured with machinery is just a bad combination. Look at the number of sharp edges on the machines, great for cutting oneself open. Now look at the soft rubber coverings on levers that can be eaten and cause colic.
I would also say that if this tractor has a front end loader and this is a new behavior that maybe there is a smell associated with the tractor. Ie. Did the son use the bucket to carry a dead animal for burial? Then its not the machine but the smell that is worrying your horse. I would say time and desensitization, but get the tractor out of the pasture.