Like any question of belief in C. S. Lewis's post-conversion writing, the question of how Susan came not to believe in Narnia comes back to how Lewis felt about a specific issue in Christianity. Susan exemplifies the fallacy of someone who certainly knows the existence of the divine, but nonetheless chooses not to believe in it. Lewis (like many Christians) believed that every unbeliever was actually like this, since the presence of God was obvious all around us. Only by active and willful denial of the obvious could a sin such as atheism be maintained, and Susan is a cartoon version of this.
Born into a religious family, Lewis himself became an atheist at fifteen, before returning to Christianity in his thirties. (J. R. R. Tolkien was famously one of the people who led Lewis to his reconversion, although Lewis returned to his childhood Anglicanism, rather than Tolkien's Catholicism.) In his memoir, in which religious issues played an extremely important role—and led to the selection of the title, Surprised by Joy—Lewis talked about how he constantly felt the presence of the divine, and it was only by actively denying it that he was able to maintain his non-belief. Whenever he let himself be distracted, relaxed, God was there, calling him back.
You must picture me alone in that room in Magdalen, night after night, feeling, whenever my mind lifted even for a second from my work, the steady, unrelenting approach of Him whom I so earnestly desired not to meet.
Eventually, he could not sustain his non-belief, and returned to his ancestral faith.
That not seeing the manifest presence of God in the world is only possible through a willful act of sinful and intentional blindness is standard Christian dogma. It was expounded by Paul in Romans 1:20 (King James Version):
For the invisible things of him from the creation of the world are clearly seen, being understood by the things that are made, even his eternal power and Godhead; so that they are without excuse:
Susan is supposed to serve as an example of the absurdity of denying hand of the divine all throughout the world, and the Holy Spirit the constant companion of the human soul. Susan had seen magic in Narnia, witnessed the very presence of God the Son (in the form of Aslan), but she chose to believe that those things were not real—that they had been games, fictions. For Lewis, this denial seemed equivalent to denying the reality of God and the stories in the Bible; God's presence and power were self evident, and only a fool or a liar could not believe in God. Yet Lewis knew that there were many atheists in the world; he himself had been one of them. He felt that those atheists, including his younger self, had been willfully, spitefully denying the clear reality of Christianity. Susan was just doing the same thing with regards to Narnia that Lewis saw so many people doing with regards to the undeniable truth of his religion.