It really all comes down to money.
The perfect illustrative example of this would be the Department of Education. States have the power to enact their own education policies and nowhere is education laid out as a federal duty. And yet, a Federal department exists.
They enter by setting policies and giving enough money to the States to follow the federal policies.
It is protected by the fact that it has a system of separation of powers with three branches that control each other and prevent tyrannical behavior from a single branch. They are also separated into local provinces and autonomous regions that are ruled by small scale governments that have some degree of independence and that could easily oppose a new form of tyrannical government.
Do to the 9/11 attacks by al qaeda.