Everytime you touch her with the towel and she stays still / calm remove it and give her a treat. She will associate the towel with the comfort of the treat.
Perhaps she doesn't like the cold / wet feel of the towel you use, perhaps she doesn't like you touching her nose.
Just with a regular wet towel.
With what are you cleaning his nose?
It's a very sensitive part of your horse so maybe it hurts her. You can use Baby wipes, good for this and baby oil to soothe her nose.