Rather than safeguarding minorities, federalism tends to create majority rule by allowing blocks to form within small regions. Although in theory the central government should step in when this happens, in practice it is often impossible to delegate the right powers to different branches of government in order to prevent it from happening. Often those with extreme views live in the same geographical area. When their power is no longer checked nationally, they may be free to institute unjust laws and discriminate against the minority.
In the US, states have often ridden roughshod over minorities in spite of the objections of the central government. One example of this is the Jim Crow laws in the southern states, which discriminated against African Americans.
Not everybody is able to move easily between states and may be trapped geographically by poverty or family concerns. It is not realistic to ask those who persecuted by the local government to change the region they live in.
Federalism can actually make life worse for minority groups, who are not protected from the persecution of small groups within regions. Parochialism is more in common is small communities.