We totally are, it's just that rationality is a tool, not a guide. If you want to work out the truth, rationality will help you do that, but if instead you want to justify a decision you already made, well, it'll help you do that too.
Hypothesis don't come from rationality either, they result from well informed intuition. All of the formality of science is about tricking ourselves into discovering our intuition is wrong using a rational series of steps even when everything in our nature is to use that ability to reason to do the opposite.
