First and foremost you need to understand roosters are intelligent. They are not just a tiny brained chicken. They are more like dogs in their perceptions of threats, and they easily pick up human words to associate with our interactions with them. Use consistent words such as you have when brandishing the stick, "back!" in the appropriate forceful tone, and like a dog they will quickly program it into their brain.
Why he is respectful of the stick and not you, is that (1) he understands the stick is an object separate from you. (2) the stick isn't acting afraid of him, but he easily picks up on the fact that you are. You see? Your fear is showing up in your outward behavior, so you need to work on conquering your fear. Continue to use the stick as you have. Just don't hit him with it. It does help to think about dog behavior when trying to understand rooster behavior. I've even found strong comparisons to human male behavior, also. It's no accident we have the word "cocky" in our language, and, ah-hem, other similar ones.
When you go out in the morning and enter the run, and he comes charging at you, hold the stick up, as chickens easily associate objects with commands, and say "back!" in a forceful tone. Then proceed into the run with slow, calm, confident body movements. If he comes charging at you again, do not stop, but keep moving slowly and confidently directly toward him, and if he attempts any aggressive actions, just keep moving right "through" him, forcing him to step aside. This is a sign to him that you have just made a dominant gesture and forced him to back down. This whittles away at his cocky self confidence, and it begins to force him to reconsider his relationship with you.
Keep that up as consistently as possible and it usually doesn't take long to see some improvement. Pop back in if you run into any difficulties and we'll give you more tips.
But be aware, there are roosters with genes for excessive aggression, and they may never respond to training. It's one reason I've stayed away from the aggressive breeds to decrease my chances of getting such a rooster.