But the seeing here is different than physical sight. When Jesus says this, Nicodemus does not understand his words. This demonstrates the case in point - since Nicodemus is not saved, he cannot understand Jesus words. Here Nicodemus thinks Christ is referring to physical birth and asks how a man can be born again physically, a second time. Jesus then explains exactly what he means.
Flesh only gives birth to flesh.
Flesh does not give birth to spirit. The wind blows where it wishes, and you hear the sound of it, but cannot tell where it comes from or where it goes. So is everyone who is born of the Spirit. Jesus demonstrates by analogy to Nicodemus that the Spirit of God is sovereign over the salvation of those He saves. So the Spirit blows upon whom he wishes to save, and then borns them again.