It would be an amazing luck if our instincts in the realm of thought could reach each and every truth. Arguing that deduction aided only by innate premises could lead us to know everything would almost certainly imply that the universe was either created by us or for us.

That being said, it is not so usual to compare logic and intuition. I feel it is a good comparison, nevertheless I should notice that most people usually set logic apart of our instincts. Perhaps we could talk about an instinct logic and a refined logic, for the same way science can overcome our initial instincts, the work of logicians theoretically could also do it.