Are you suggesting that instinct should always be questioned?
To put a different spin on it, magicians and illusionists have long played with our instincts in order to fool us. The whole point of the scientific method is to question our instinctive reactions to phenomena around us.
The emergence of the modern scientific method came about because of a battle between the Rationalists and the Empiricists. The Rationalists proposed that we could reason our way to a conclusion in an instinctive manner. The Empiricists argued that our instincts were not reliable, and we should therefore verify our conclusions through experimentation and empirical facts. The Empiricists won, and what we got out of it is modern science.