The prior response to your question is text book. Actually, a lot of people in an organization can affect your audit by placing obstructions in your way and controlling what you look at, how you look at it, and when you look at it. It all depends on the organization. It doesn't matter what the IIA Standards or Audit Charters say. In reality, many audit committee chairs are selected by the CEO who is often chairman of the board. So, understanding the politics will take you a long way in first, keeping your job, and second, getting your job done with minimal disruption to the auditee and your ego.
When you are auditing, always be aware of who you are (an auditor) and how you are perceived. You can't change it but you can try be empathetic to the people you are auditing. Do this, and you will gain their respect and trust. Even if they don't like the results of the audit, they will respect you as a person and professional and will treat you with accordingly.