I think the theory is that people vote for their president and he is elected because they believe in his policies and leadership. Thus, he is the decision maker. Policy advisors are just that, advisors.
Those who have been in government for 20, 30 years believe THEY know what is best. They are unelected, but, they've been around so long that they promote their tenure as somehow confirmation that they are the most knowledgable on a subject and have all the answers.
Presidents disagree with advisors all the time, but because Trump is an outsider and disrupter he is attacked since the Establishment can't use the advisors to control and effect policy.
Bill Clinton famously disagreed with the CIA and even shut their Director out or gave him little time. It was frustrating to the C.I.A but what could they do? He is elected, they are simply doing (or were trying to do) their sworn duty, but the president decides what to pursue or even if he will meet with the director to eve be updated or not.
We know that the Kennedys had issues with J Edgar Hoover. Really they openly despised him.