I understand the coach is the ultimate authority, and the buck stops there. Also, there is likely more to the story, and not much background was provided, so the coach likely had addressed this, and was now teaching a lesson.
My stance as it relates to shaking off signs, is that as others have stated, the only person ultimately responsible for the outcome of every pitch thrown, is the pitcher. I have always told my pitchers, and my son - if you can't throw the next pitch with 100% confidence, then don't throw that pitch...it is always "your pitch" to throw. I had an ex CWS pitcher from Cal State Fullerton, tell my son once - "if you can't throw the next pitch with an "F-you" behind it, then don't throw it".
In this case, either the coach has way too big of an ego, OR there have been problems in the past where the pitcher was not executing with the pitches "HE" was choosing, and the coach was trying to help him learn how to work a batter.