It's in the job description of an assistant coach to be frustrated with the head coach. That is just the way it is. As the above poster mentioned, if you feel that strongly about it then leave and find a new position.
The job of an assistant is to support the head coach and execute any assignment he gives you to the best of your ability, regardless of whether you agree with it (as long as it is not unethical).
Work hard, develop a good working relationship with the HC so that you can build your resume and have a good reference and move on at the end of the year. If you stay there for more than a year and you develop the trust of the head you can talk with him about changing things next year. But if this is your first year there... keep your mouth shut and do what you're told.
My last piece of advice is to stop thinking you know better than everyone else. Every kid out of college thinks they have all the answers (I know I used to). I'm not saying that your HC is right, I'm just saying that you need to get over yourself a bit and be thankful for the opportunity you have instead of trying to undermine the head coach. Take a step back, observe, watch and learn. Maybe you can pick up on some things you didn't know before.