^ ...?
Anyways, my explanation is that what and why are different questions.
When you ask what something is or isn't, the only thing you give is the "something". That's only one constant, and everything else is a variable which can change. However, when you ask why something is, you're giving the "is" and the "something", so you now have two constants. Therefore, they have to agree, or your question doesn't make sense.
In "What is the sky?" and "What isn't the sky?, "the sky" doesn't have anything it needs to agree with, so both are valid questions.
In "Why is the sky blue?", "the sky" and "blue" agree, so it is a valid question. In "Why is the sky not blue?", "the sky" and "not blue" don't agree, so it doesn't make sense.