As long as a person lives, there will be a part of his essence that denies the existence of Hashem, not because that part is rebellious or because it wants to do anything wrong, but because it is incapable of seeing anything that isn’t physical. The more a person grows, the more clearly he relates to his spiritual side, and the less the Nefesh Ha’Bahami clouds his vision. However, as long as I am housed in a body, this darkness remains a part of me.
The answer to the question seems to be that Noach was a real believer. He had a powerful, unwavering belief that everything Hashem said would happen would indeed come true. But that was only half of him. There was another part of Noach that didn’t see Hashem, couldn’t relate to Him, and couldn’t see anything beyond the here and now. That part denied that there would ever be a flood.
Even an ish tzaddik who spent 120 years engaged in teaching that Hashem was going to bring a flood, was still a human, and as such, he couldn’t fully see it happening. It wasn’t until the rain started that it became real to him, and then he went into the tayvah.
This concept is very relevant to us because no matter what level a person has reached, there will always be a part of him that denies anything spiritual. There will always be a part of me that feels alone in this world because it cannot see Hashem or even relate to anything that is not physical. However, there is another full dimension of me that intuitively knows Hashem is right here, running the world, involved in every detail of my life.