Everything can be misused, that doesn't make everything bad per se. Saying that hierarchies must be mitigated (because they are bad, I assume) is unreal.
Good thing I didn't say that, then. What I said was that we must look at what's natural and decide which bits require amplification and which require mitigation.
And of course saying that hierarchies should be mitigated is far from unreal. It was the central message of the people who started America. They put a great deal of effort into checks and balances on power both at the federal level (between the 3 branches) and in having local, state, and federal governments, none of which have a hierarchical relationship. They put a strong emphasis on individual rights, which are counter-hierarchical as well. And let's not forget the freedoms of press and political speech, first among the Bill of Rights, which is very much a check on hierarchy.
Federal law does not a priori supersede state law. The Tenth Amendment to the US Constitution reserves _all_ rights not explicitly granted to the federal government to the states and the people. The Civil War was fought, in part, over this contention between the power of the federal government to emancipate slaves and the power of the slaveholding states to continue to allow the practice of slavery. In more modern times, certain aspects of the constitution have been interpreted more and more broadly to allow e.g. the regulation of medical products under the auspices of regulating “interstate commerce” (even if said products are only ever sold in a single state — they can be transported across state lines).
From this system design, you can deduce that there _does_ exist a hierarchy in the theory of US government — the Constitution is the law of the land and all other actors and subsystems are subordinate to it. Modifying the Constitution requires significant effort at multiple levels of government usually including (by state law) extensive popular support and supermajorities of representatives.
The answer from silentOpen is excellent, but I wanted to add a few things.
Hierarchy is the rule of men, not of laws. So even if there were a hierarchical relationship between bodies of law, that doesn't require a hierarchical relationship between people.
In the US, federal law can supersede state law, and state law can supersede county and city law. It does have to be written that way of course. In practice, many laws are written to allow jurisdictions to self-regulate within broad limits. For example, in California it's legal to open a marijuana store. But localities get to decide whether it happens in their city. And it's technically illegal federally, but that's currently unenforced.
But the president has no direct authority over governors, and governors have no direct authority over mayors. However much Trump dislikes a variety of San Francisco policies, he cannot just order them changed. Instead he would have to persuade both the House and Senate to pass a law, and San Francisco could challenge that law in the courts.
