The behavior you have described is self rewarding. You accepted it, erroneously labeling it as instinctive and protective, and took no pains to make him to stop. Now, you have a problem.
The behavior is self rewarding in that, he's heard something and barked, growled and acted like a vicious deranged animal... then the "danger" went away! Hey! If I bark and terrorize, I can make it go away! Do you see how it's self rewarding?
YOU have a long haul ahead of you, as by now he's already learned, In his mind at least, barking works! He can chase anything off by barking.
You must begin to reward any moment of silence. The best way is to get a clicker and some high value diced treats (leftover steak, pork chop, chicken breast, cheese, hot dogs). You can have him leashed to you so you catch it every time, but it's not totally necessary.
Reward any silence with an imediate (cues him in to WHAT he's doing at that moment) click, followed by a treat. You will pique his interest. Repeat for any moment of silence you get. Remain calm.

"Mmmmmm! What do I do to get more of those treats?"
Next session: Add the word "stop" or "enough" or "no more." Then click and reward any silence you get. Repeat, repeat, repeat. Don't give up! He's smart enough to overcome this uncontrolled idiocy. You CAN do it. Be consistant, and very careful to click the second you hear any S-I-L-E-N-C-E.
Told the story before: Rave became perturbed over a motorcyclist with a mirrored helmet. She'd had motorcycles follow us before. But this one had a mirror and it reflected and shone all about, so she barked! For what seemed like 10 minutes I could not get her to stop.
I arrived at class frustrated, headachy, and miserable. My instructor, said, "Just click the silences." (We do our agility training with a clicker) It made perfect sense! That very night...the same cyclist was behind us again! What luck! I did it and had her attention in the first click. My dog is completely clicker trained, so don't expect as quick a response. Within 4-5 click/treats she
knew what I wanted.
It may take weeks. But you CAN change obnoxious behavior. It takes consistancy, and determination, and a right method. This method works because: 1) It targets the correct behavior. 2) It rewards the correct behavior. 3) It makes the dog figure it out. Dogs learn better if they have to think. And, 4) It substitutes an acceptable behavior for one that is not.
