Those who say religion has nothing to do with the mind, or reason, are wrong. Why should this be, when reason has been bestowed by God? Religion has been sent by God and our minds too have been given by God. Then how is it possible that religion will have no relation to the rational mind? The use of our reason should be according to a framework. 
What is the framework? It is the Quran. The Quran gives us guidance on how to think. For example, the Quran says: "You have been granted but little knowledge." (17:85)
What is the meaning of little knowledge?
Through your reason you can have little knowledge, not complete knowledge. This world lies within space and time. In this world we use our reason to understand matters. But there is another world which is beyond space and time. We do not have the power to know about that world. Here, the Quran gives us a principle: use your rational minds to understand the meaning behind this world which is within space and time. What lies beyond space and time cannot be understood by human reason. God's existence lies beyond space and time. You cannot know about God's being. You can know about God's creation, His glory and His attributes. The use of the rational mind is extremely important in religion. But we must know that reason has its limitations. It is not true that human reason can know everything without limits, even what lies beyond space and time. This is how we have to apply our reason to understand God and religion.