So why is it bad when the Federal Government tells a State what to do, but it's a-okay when the State tells a City what to do?
Because of the 10th Amendment: The powers not delegated to the United States by the Constitution, nor prohibited by it to the States, are reserved to the States respectively, or to the people.
There's a pretty limited set of powers for the federal government enumerated in the Constitution. Probably 80% of what the Feds do isn't really allowed by the Constitution. They only get away with it because judges do their wink-wink bit and let things slide, frequently under some tortured interpretation of the commerce clause.
While there is a common belief that local control is "A Good Thing(tm)", any protection cities would have from State government depends on laws from that state.