Why was Big E a xenophobe?
From the HH books we've learned that the Emperor's great crusade was one of reason, logic and scientific pursuit that threw away all superstitions and theologies.
Yet at the same time it was extremely xenophobic. If there is one thing you can state with absolute certainty about racism and bigotry is that they are completely irrational bordering on delusional. So not exactly shining examples of logic and reason.
Now Big E's main goal with the crusade was to safe guard mankind's destiny among the star so it makes sense the dangerous aliens like for example orks, tyrnids, necrons and even shifty eldars would get a bolter bolt to the head.
But what if the crusade had come up against aliens like the tau that isn't inherently hostile. That have similar overall goals of making the galaxy a safe place, would prefer diplomacy over warfare and isn't opposed to peaceful cooperation, coexistence or even an alliance.
The xenophobic result we could expect from the crusade even towards an alien race of that type would not be the reasonable and logical approach Big E claimed the crusade was about.
So why was the Emperor so xenophobic?