Federal governments are not immune to tyranny, although they may slow its inception. The most prominent example of a federal state turning to fascism is Weimar Germany. Upon getting elected Hitler simply revoked the powers of other sovereign bodies. 
Sovereign states typically retain the right to revoke the powers of its constituent bodies at will, especially in emergencies. When states overstep on political issues which are unpopular with the central government, their desires are frequently ignored. Many political theorists believe that cultural norms and moral values are the only real barrier to dictatorship. 
The central government’s sway over the national army is often the trump card which allows them to take power. Even if federalism allows for checks on the military it cannot stop fascists from raising their own militia to override the established order.
History shows that federalism does not make a democracy immune to dictatorship. Federal powers can be revoked by the central government, who often hold sway over the military. Powerful and charismatic dictators often find ways to raise loyal forces that bypass the separation of powers. Local government can also be tyrannical or unjust.