1) You sense a clear disconnect between your stated faith and the nature of reality. This happens in a few different ways.
a) The Bible portrays a relational God that intervenes in the world and confirms His presence in our lives. If you’re feeling lonely, unconfirmed, and unguided, it’s probably because you are!
b) Over time it becomes increasingly clear how little you actually know in this regard. This is when you must reluctantly admit that your knowledge of God and supernatural worlds may actually be insufficient.
c) Since insufficient knowledge exists then you are now more willing and open to admit uncertainty.
2) You suspect that prayer has little to no correlation whatsoever with the events that actually unfold in your life. You rightly discern that to not pray carries the same degree of pattern confirmation and/or disconfirmation.
3) As you are confronted with the massive variety of thought that exists within your own religion as well as within all religions you start to recognize how astonishing it is to think you are right while all or many others are wrong! Particularly in the area of special knowledge that God is said to give to the faithful. If many other religions claim to have special knowledge of their gods then your own position tends to diminish in its own perceived uniqueness.
4) When well intentioned obedience to a holy book becomes harmful or destructive in its application you realize that something doesn’t seem right. For instance: The New Testament contains warnings about eternal punishment for not conforming to its mold of righteous thoughts and actions. It is therefore considered essential for believers to pronounce impending doom upon the world. All that one needs is a Bible and a platform to speak. Nothing else is required so as to distinguish this set of warnings from what is contained in other holy books.
This also sets up a dichotomy between those who follow God and those who don’t. There is an in group and an out group. This becomes very tribal in the end. If you don’t join our tribe you are defective and deserving of punishment and death. The believer says, “I don’t wish any harm on you, this is your opportunity to see the love of God. I warn you because I love you.” I think there are two things that prey on the believer’s mind in this instance. 1) The believer is filled with actual fear that to not conform to such and such a God’s desires will in fact incite wrath and eternal judgement. 2) The other factor that comes into play here is self-deception. The believer actually thinks that he or she has an inside scoop into the mind of God. My holy book is the perfect inspired message of God. I recognize this and can therefore speak with some measure of authority on this matter.
5) As you consider the universe and our world you come to see that there is more than one way to understand design. Design need not imply a God in the sense that natural processes appear to be unguided and unconcerned with regard to harboring life. Over billions of years galaxies would come and go. Supernova after supernova. Collision after collision. Stardust and their particals unassembling and reassembling slowly yet constantly. Millennia after millennia multiplied of galaxies having no tolerance for life at all. Another possibility being that some galaxies would begin to form life at its most vulnerable stage only for it to be extinguished by another heat death. After an untold amount of time and chaotic fluctuation of almost every condition imaginable carbon based life finally found a foothold. Earth may not be the only place where this has occurred or is still occurring but what we do know is that even a world with the right set of ingredients is still not benevolent or concerned about life in the slightest. Afterall, something like ninety-nine percent of all species that have ever lived on earth have gone extinct! Some designer! Some purpose! How humbling it is to know that we have even been given this small window of time to enjoy a universe that otherwise doesn’t appear to care whether we remain or go away forever.