Consider whether you are giving messages of disrespect to your boss in any way. If you are struggling with authority issues, it may be difficult to let small conflicts go. Choose your battles. It is in your best interest to allow this person to feel in control. Small items do not matter.
Big ones do.
Clarify the differences for yourself. If you feel the need is justified, do speak up. But do so in a respectful manner. If you have come to terms with the fact of your boss' authority over you and clarified boundaries, mutual respect can be established. Some peace offering may be beneficial.