Skeptics have always been around. God is not afraid of our questions, He welcomes them. If we look back in the Old Testament we can see God taking the time to talk questioning children. In the Book of Habakkuk we find a prophet in a rather heated exchange with God. He cries out, > "How long, O LORD, must I call for help, but you do not listen? Or cry out to you, "Violence!" but you do not save?
Why do you make me look at injustice? Why do you tolerate wrong? Destruction and violence are before me; there is strife, and conflict abounds." Questions facilitate conversation and without honest communication any relationship would die. As a skeptic I am always asking questions about something. While this can often lead to better understanding it can also lead to analysis paralysis. That's when we think something to death. God is not angered by our questions but he does not want us to get stagnate because of over-thinking.
Many times this is caused by fear.