What's the (metaphysical) difference between Good and true intuition, and the mainstream evil nonsense?

Everybody's belief is ultimately rooted in intuition. 

What, then, is the difference between Good intuition that leads to a Romantic Christian commitment (if Jesus's promises are what the person most deeply desires); and the kind of evil-affiliated, totalitarian-believing stuff that the mass majority of the West have chosen?

The difference is that: most people's intuition is rooted in some-thing that denies the validity of the intuition itself. 

For instance; many people (it seems) have an intuition that the universe is purely material, happened entirely 'by physics', has no purpose, and that my own life arose through the blind algorithmic processes of natural selection and therefore has no objective or eternal meaning. 

Thus my thoughts, my deepest and surest convictions, can have no possible objective connection with reality. Intuition is just a temporary, subjective, meaningless emotional response.  

In other words, the intuition is rendered meaningless by its own conviction: because my intuition is that intuition is meaningless! 

But this self-refuting incoherence is obscured by a somewhat roundabout argument, with several steps - and few people choose to think for long enough or sticking to the subject such that they realize that their beliefs are self-contradicting. 

Good intuition is different because Good intuition is coherent. 

Good intuition is in-place when there is an intuitive belief in a scheme of understanding - i.e. a metaphysics - that itself explains why the first intuition is valid.

So the first intuition is that the nature of reality itself explains how it is I personally (here and now) can intuitively understand reality. 

In other words, the first Good intuition if of a metaphysical scheme that itself explains how true personal intuition is possible. 

The confirmation of this first intuition comes when this metaphysical scheme that explains the validity of intuition is itself intuitively affirmed. 

Thus, in Good and true intuition - we have coherence of many mutually-supporting intuitions, and of the scheme-itself of mutually-supporting intuitions as-a-whole.