Wrestling With Faith

Is it okay to question your faith?

I have had this question asked many times and worded in many different ways.  The main idea of the question is always the same which I stated above and we are going to seek to answer.

First Hebrews 11:1 says, "Now Faith is confidence in what we hope for and assurance about what we do not see."
James 1:5 says, " If any of you lacks wisdom, you should ask God, who gives generously to all without finding fault and it will be given to them."

Faith is our belief in God, the Bible, and the statements of our Christian faith.  The hard part for people is that God cannot be definitively proven or disproven.  At the sametime, nothing in science can be definitively proven either.  The main point of the scientific method is that science seeks to show probability and always leaves room for growth in knowledge.
When it comes to God there should also be growth.  In order for us to grow we need to ask questions and seek to find answers.  This means that at times we may develop doubts. God welcomes our questions.  This is why in the book of James God says if you lack wisdom to ask God and he will give us wisdom.  
God didn't create us as robots that just do blindly as we they were programmed.  God created us with the ability to reason and to make our own choices.  This means that we will question and even doubt at times but God wants us to seek Him and ask Him and in doing so God wants to give us the answers and develop a deeper relationship with Him.  This means that some may choose to not to believe or change this minds on what they believe. God's hope in giving us the ability to reason and ask questions is that we would come closer to God.