About Doubt

An ignorant man is lost, faithless, and filled with self-doubt;
A soul that harbors doubt has no joy, not in this world or the next. (Bhagavad Gita 4:40)

Doubt is an unavoidable part of the life experience. And that is a normal part of one's spiritual journey also. But how it is painful! It is similar to tunnels of darkness without any gleam. At this moment it is difficult for understanding but these times need be only moments in one's journey and attestations to the spiritual energy to be discovered within faith. Doubt is the impetus for spiritual renewal, stimulating one to question and to search for answers. It is not a place of permanent repose.
Yes, the doubt is some sort of tabu in religion. But we are human beings, who feel the need to reflect on their belief. Any aspect of human life can be subject to reflection; religion is no exception. Even those who consider themselves with no religion may have moments of doubt about their atheism. Skeptical or inquiring doubt can often be beneficial. For instance, in many spiritual traditions you are encouraged to be skeptical of blindly accepting beliefs and to explore through your own direct experience what is true.  For example, in Islam, Al-Ghazali experienced a deep crisis of scepticism; he doubted about his senses and his knowledge, but he claimed that doubt was his habit to search for the true reality of things. Thus, doubt and religion cannot be separated, and everyone should look for the truth to better understand his convictions and answer his doubts.
The similar story has occurred to one of Christian apostles, Saint Thomas (or Doubting Thomas), who refused to believe that the resurrected Jesus had appeared to the ten other apostles, until he could see and feel the wounds received by Jesus on the cross.

"The Incredulity of Saint Thomas" by Caravaggio

Also, Saint Peter almost did walk on water until he doubted. We, the flesh will always be in doubt. It's our character. To overcome it, yogis in India still go into the forest to discover spirit for themselves, and the same is true of the Desert Fathers in the Christian tradition.
In Hinduism, we can verify our knowledge in three ways: by sruti, the sacred scriptures; yukti, the knowledge or reason; and by anubhuti, or personal experience. But separately, each of these points also can give in to our doubt. For example, we can consider that scriptures describe experience of others and by the limited means, the reason solely can develop thoughts infinitely, and personal experience can be deceptive and delusive, and we can always wait some decisive proof. So, to be assured, our knowledge or personal experience must be testified to by the scriptures, and  corroborated by reason. Then, without a shadow of a doubt, you see. An analogy to this which is often used is if someone holds up a flower in front of your face, and your eyes are open, and your mind is backing them, do you see the flower or not?
Doubt is an element of risk that must be affirmed by courage, but it can return us from despair to a new content of belief. After all, Doubting Thomas does not stay a doubter. With hope, I want to remember again the words from the Bhagavad Gita: When righteousness is weak and faints and unrighteousness exults in pride, then my Spirit arises on earth.