Listen to Gene Roddenberry talk about his vision of the future, and humanity, and then read Thus Spoke Zarathustra. From the Augments, to Federation ideals. The Trek universe is littered with references.
Not seeing it. The Augments are bad guys. The Federation's "ideals" are mutable and somewhat generically "good". GR was mostly believing his own hype.
I honestly don't think you have read the book.
Well for starters, there's the misconception that the Ubermensch implied eugenics. For example, Hitler, master Aryan race, ww2. For star trek reference, Khan, the augments, eugenics wars.
Then we have egalitarianism in relation to the Ubermensch. Federation with an idealistic society.
The federation also embodies the notion that god is dead. Where purpose and values are not found through other worldly influences, but through our own goals and the common good.
The Ubermensch, or the over human, is an ideal to strive towards. To better ones self and society. And not succumb to flights of fancy. Aiming towards being infallible essentially. The show has preached just that time and time again between federation values, and the prime directive. It's literally the federations mission statement.
Some of his other themes:
Will to power was a commentary on society. An egalitarian state signifies a departure from the desire to accumulate, and a drive towards self actualization. The federation represented an egalitarian state, where the idealism had transcended that of contemporary society's. Again, as it was mentioned quite frequently in the show.
The show also criticized herd mentality, and emphasized the importance of individualism.
The prime directive, and all the circumstances that occur because of it, is also a direct representation of the Genealogy of Morals.
If you're familiar with his works, I honestly don't know how one cannot see it. Nietzsche's finger prints are all over federation idealism.
edit: P.S It's not like it's conjecture that Roddenberry read Nietzsche. He named an alien race after Nietzsche on Andromeda.