In the Contemplation Sutra (one of the sutras of the Pure Land School) which tells the story of Queen Vaidehi's acceptance of the Pure Land of Amida Buddha, she is visited by the Buddha and his disciples Ananda and Maudgalyayana. They do not simply get a prison pass and walk in the prison, but they appear to her seemingly out of thin air. The Buddha shows her a vision of the Pure Land, and Vaidehi decides to be born there. In many other sutras, the Buddha manifests supernatural powers and accomplishes deeds which could be described as "miracles" or, activities which defy scientific laws.
Much of this can disturb readers who are expecting a more "rational" form of teaching (the idea of Buddhism as only philosophy comes to mind), and who could be uncomfortable with concepts like "miracles," which we assume to belong solely to the Christian tradition (yet even some Christians, like Thomas Jefferson, was uncomfortable with this)! However, these can be present in many other religions, including Islam.
How can we understand the sutras with their descriptions of incredible beings, and abilities manifested by the Buddha and his disciples? Should we just accept them "literally" that these beings and powers existed in history, or just dismiss them as elaborate yet impossible depictions created later by imaginative scribes? Should we accept one explanation without question, and then deny absolutely the opposite opinion? If the sutras contain "impossible" depictions, how can it be reliable? Where is the truth in its pages? Can it speak to us in today's worlds, with 21st-century issues?
I believe that the answer may lie in between these explanations. The sutras Pure Land or other schools, were not written to be a only a dry, historical account of the Buddha and his teachings, they were also written to convey the idea of the Buddha's uniqueness, to encourage devotion and adherence to the Pure Land teachings, and the wider Mahayana tradition. In the Lotus Sutra, it is encouraged to follow the teachings within this particular text, while other sutras say that this sutra is best. Is one false and the other true? Yes, some Buddhists have argued one is true and the others all heretical, as the Japanese monk Nichiren did in favor of the Lotus teachings. Other monks have made arguments for the validity of the sutras they follow, over others. Depending on the school, one sutra, or several, is preferred over others.
The sutra is not only a primer of "philosophy" but a text that is, perhaps pardoxically, irrational. It is meant to take us to a separate level of understanding, perhaps similar to the purpose of the Zen koan. When we read the sutras, we also read with the mind of faith. This mind of faith is not the mind of "blind faith" (of which many people criticize organized religion for) but rather the mind of opening the mind to the Buddha-Dharma. We may compare queen Vaidehi's example, of receiving the manifestation of the Pure Land in her mind.
However, we have to combine our reason with our devotion TOGETHER, to read the Buddhist scriptures. Simply stating that everything in the sutras is "literally" true or that everything in the sutra is merely smoke and mirrors for another "intellectual" meaning is falling to another extreme, which we should always try to avoid. A Buddhist has this responsibility, and should carefully consider thus the ways to read the sutra for himself/herself. Many individual Christians struggle also with reading the Bible, and take great care how they approach it as both a literary text and as a devotional text; as the sutras are our "holy text" we should take an approach of equal respect and critical reading towards the sutras (which exist in several different versions). Not to do this can lead us to error and the calamities of doubt, or perhaps worse, to what we see afflicting the religions today. Most people only see this played out on our TV screens. Seeing it in person, in Afghanistan for example, leads me to understand that how we read the sutras is crucial to our own understanding of why it is so important to read the sutras, with always the goal of the Buddha in mind - to achieve peace and compassion, beginning with oneself.