"it doesn't seem like that crazy of an idea"
refers to the idea that 'all humans are inherently good'.
But in that sentence, the 'it' refers to the idea that 'all humans are inherently good', and not the word 'idea'.
And 'his' refers to Abraham Maslow's.
Sure, it doesn't seem like that crazy of an idea, but it was for Maslow's time.
This means that the idea was considered 'crazy' during the lifetime of Maslow, but not necessarily now (or earlier).
You had the third doubt because you mistook the reference of the word 'idea' as Maslow's idea, in the sentence "Sure, it doesn't seem like that crazy of an idea, but it was for his time.".
As mentioned above, in that sentence, his idea is referred by the word 'it'.
The phrase "..that crazy of an idea" talks about his idea (Maslow's) is not a very crazy idea, when compared to all the general ideas that people have.
This is very hard to explain, but let's assume that there is a huge pile of ideas. In that pile, there are good ideas, bad ideas, crazy ideas and all the ideas you can think of.
Now, Maslow had an idea, which was that all humans are inherently good. This idea was not a crazy idea, at his time of existence. In the sentence, 'it' is Maslow's idea and the word 'idea' is the huge pile of ideas. So, when compared to the crazy ideas in that pile, this idea was not all that crazy.
Note: This is a little hard to follow, but feel free to ask via comments if you need a little more clarification.
"His work was not that bad of a musical".
This means that the work done by the subject, which happens to be a musical is not that bad, in general.
This can be rewritten as: "His musical is not that bad."
The extension is a simple usage in English.
"He isn't that bad of a man."
Which simply implies that he is not a bad man.
To your question #3 - "I don't know what is the difference between "that crazy of an idea" and "that crazy idea", there is no actual difference. This is just a usage in English.