Our intellects might be capable of arriving at the conclusion that God exists. However, we are, by nature, more than intellect. We have other aspects of our nature that might rebel against believing in a God to whom we owe our being and who places moral demands on us. Consequently, there is, in our nature, something that inclines us to deny that God exists and, consequently, to refuse to believe something that our intellect tells us is certain--or, in many cases, that refuses even to allow our intellects to consider seriously the evidence for the existence of God.
I think this is a good point.
The full paragraph from Humani Generis I quoted in part in my last post runs like this:
It is not surprising that such discord and error should always have existed outside the fold of Christ. For though, absolutely speaking, human reason by its own natural force and light can arrive at a true and certain knowledge of the one personal God, Who by His providence watches over and governs the world, and also of the natural law, which the Creator has written in our hearts, still there are not a few obstacles to prevent reason from making efficient and fruitful use of its natural ability. The truths that have to do with God and the relations between God and men, completely surpass the sensible order and demand self-surrender and self-abnegation in order to be put into practice and to influence practical life. Now the human intellect, in gaining the knowledge of such truths is hampered both by the activity of the senses and the imagination, and by evil passions arising from original sin. Hence men easily persuade themselves in such matters that what they do not wish to believe is false or at least doubtful.
I had been thinking of the difficulties and admixtures of error in coming to certain knowledge of God by reason as being due to our all-too-fallible intellects, our philosophical mistakes being akin to arithmetical errors.
As the Pope and the penitent point out, though, we also have all-too-peccable wills that prevent us from arriving at certain knowledge as surely as a student's disinclination to concentrate on his math homework prevents him from getting the right answers. (Of course, few students are so contrary that they want to get the wrong answer, but they might -- if, say, that insufferable know-it-all next to them says the answer is 15,647.)