Actually it isn't how you look at it. Being a fictional work, there is no ambiguity. he creator of the universe within which all of the authors write clearly states that The Emperor and the Imperium are the good guys (although oftentimes anti-heroic in the same way the Punisher is an anti-heroic good guy) and the Chaos powers and followers are the bad guys (sometimes in the way that zombies in zombie movies are bad guys, other times in the same way that Michael Corleone is a bad guy.)
I don't agree with that at all. 40k is all about ambiguity and personal interpretation, it's always been that way. If an individual interprets the setting as the Emperor being a mindless tyrant and Chaos being a worthwhile elemental force then thats their interpretation, and it's no less correct than yours or mine.
Often the Emperor may be portrayed as the 'good guy' but that's merely because most codicies and BL novels are from an Imperial point of view, it doesn't universally make it the case.