The Christian walk is not one of blind faith. God does not say we cannot question Him. He calls out our intent, though, when it is merited as it was with Job. But note how Jesus responds to Nathanael’s question:
Nathanael said to him, “Can anything good come out of Nazareth?” Philip said to him, “Come and see.” Jesus saw Nathanael coming toward him and said of him, “Behold, an Israelite indeed, in whom there is no deceit!” – John 1:46-47, ESV
Nathanael’s question is well-deserved. Nazareth was a neighboring village and it likely didn’t have a good reputation in Nathanael’s eyes. Based on Jesus’ response, we learn that Nathanael was seeking after purity and integrity and the reputation of Nazareth was enough to cause him to be skeptical towards his friend’s claim. He did not want to be seen as wanting before God by following after something sinful. Therefore, Nathanael questioned.
Jesus didn’t call out Nathanael’s question. The intent behind the question was sound. God didn’t call out Gideon, either, with the fleece twice used to confirm God’s command for his life. The reason God had no issue with these men’s questions is because they intended to discern truth. They were asking questions for the right reasons.
Our God is fine with our questions if our intent is sound. He encourages us to meditate on His Word. If we do so diligently, we will have questions. If we attempt to live out our faith dutifully, life will cause us to have questions. If our questions are founded and asked in a dogged pursuit of God, Scripture reveals He is fine with that.
Do not be afraid to ask questions. Any who would tell you questions are wrong doesn’t truly understand why there are so many examples of men and women pursuing after God who ask questions of God. We are to question. Here’s a thought: if we do not ask questions, don’t we leave seeds of doubt which can grow within us? How does this honor God? We are to glorify God and enjoy Him forever. At the very least we should be asking, “God, how can I personally glorify you most of all?”