User blog comment:Master Sima Yi/Assassins vs. Templars: "good vs. evil"/@comment-4220817-20130121204604

The Templars throughout the Crusades and Renaisance were generally ruthless and power-hungery, though there are notable noble exception. As their understanding of the First Civilisation increased, they dedicated themselves to protecting mankind because they recognize their subservant nature.

I think this is where the difference lies between the Assassins and Templars, the whole "Good vs. Evil". The Templars view and humans as animals in need of guidance and control, hence see themselves as protectors at any cost, to put it negatively that makes them tyrants/evil. The Assassins however oppose this because they have faith in free will, this makes us perceive them as being noble and heroic.