The Mind that accepts the Buddha, Dharma and Sanga as the ultimate objects of refuge arises from the causes of developing fear of the suffering of the lower realms and faith in the potential qualities of the objects of refuge to protect us from our fear. Our faith enriched with wisdom and based on logic and reasoning. It should arise on the basis of understanding what we are taking refuge in, not just because  Buddha is described as having the major and minor marks, and so forth.

From: "Practising the PATH" by Yangsi Rinpoche