The reason our sensus divinitatis — our God faculty — doesn’t always automatically form belief in the Christian God is the same reason for all our woes: the ravages of sin. 

Sin — that innate disease — has damaged not only our wills (that is, what we want) but also our minds (what we think). Of course, in most people the sensus divinitatis isn’t completely destroyed; it usually functions to some extent, which is why most people believe in something supernatural. 

But according to traditional Christian theology, to the extent that a human doesn’t believe in the Christian God, the sensus divinitatis is badly damaged.