God’s Response to Human Questions in the Bible
By Elizabeth Prata

God came to Moses in a burning bush. The bush was burning but not consumed. Moses saw the spectacle and his amazement awakened, He turned aside to view it. That’s when God announced His presence and said Moses was standing on holy ground.
Just think on that for a second. What if you were going about your daily life, and by the side of the road you saw a car that was burning but not consumed. Would you stop? Would you believe it if God said I AM to you?
Anyway, we know Jesus is not making appearances these days but we tend to take for granted the shocking biblical moments when we read about when the supernatural breaks into the mundane. ‘Oh yah, that’s the burning bush’ we think. But pause and consider what it was REALLY like for Moses.
God told Moses what Moses must do. Yet, Moses wasn’t too sure about these marching orders. He questioned God in Exodus 3 in a series of questions. He asked several reasonable questions and God patiently instructed Moses. It was only the last one, where Moses’ questions turned to objection, that God became angry. This is instructive for us.
1. But Moses said to God, “Who am I, that I should go to Pharaoh, and that I should bring the sons of Israel out of Egypt?” (Exodus 3:11).
2. Now they may say to me, ‘What is His name?’ What shall I say to them?” (Exodus 3:13).
3. Then Moses said, “What if they will not believe me or listen to what I say?” (Exodus 4:1)
4. Then Moses said to the LORD, “Please, Lord, I have never been eloquent…(Exodus 4:10a).
5. But he said, “Please, Lord, now send the message by whomever You will.” (Exodus 4:13). Other translations say that Moses said ‘Send someone else’.

NOW the Lord became angry. Moses’ questions, while initially reasonable, drifted to faithless objection. He wanted out from the responsibility. There was a consequence to his attitude, as Jamieson-Fausset-Brown Bible Commentary states,
“The anger of the Lord was kindled against Moses—The Divine Being is not subject to [boiling] passion; but His displeasure was manifested by transferring the honor of the priesthood, which would otherwise have been bestowed on Moses, to Aaron, who was from this time destined to be the head of the house of Levi (1Ch 23:13).“
Mary asked a reasonable question to the angel Gabriel informing her that she would soon be pregnant. Very reasonable! She wondered about this, an event that had never happened before and never would again. “How can this be,” Mary asked the angel, “since I am a virgin?“(Luke 1:34). In her innocence, she was not rebuked. Her question was sincere and pure.
Habakkuk asked God about the timing of God’s plan, and was patiently instructed. The Prophet was earnestly inquiring. More at Habakkuk Questions the Lord, a Ligonier article.
But Zechariah the father of John the Baptist questioned the angel Gabriel too. Why was he punished and Mary wasn’t? Because of all people, a priest of God should have remembered the same angel Gabriel brought a message to Daniel. He should have remembered that Abraham and Sarah bore Isaac in their dotage just as Gabriel said Zechariah and Elizabeth would bear John. Worse, Zechariah asked for a sign- “how shall I know this?” and thus, demonstrated his unbelief. Gabriel replied exactly that -“because you did not believe my words, which will be fulfilled at their proper time.” (Luke 1:20b).
Where Mary accepted the news in submission, Zechariah’s question showed unbelief, so he was punished. JC Ryle here on Zechariah’s question: Zechariah’s Unbelief .
The Pharisees asked a whole bunch of questions. Their questions were insincere, dishonest, and came with an evil agenda (they were trying to trap Him, test Him, and destroy Him.)
God encourages us to ask questions. If we are truly wondering, seeking, grappling with the enormity of it all, God understands. He answered Habakkuk and Mary. He was patient with Moses (to a point). Jeremiah, Job, and Elijah all asked God to let them die. They were not rebuked or punished. Instead, GotQuestions explains:
Through the prophet Jeremiah, God says, “Ask me and I will tell you remarkable secrets you do not know about things to come” (Jeremiah 33:3, NLT). How could it be wrong to question God when Jesus Himself encouraged, “Keep asking, and it will be given to you. Keep searching, and you will find. Keep knocking, and the door will be opened to you. For everyone who asks receives, and the one who searches finds, and to the one who knocks, the door will be opened” (Matthew 7:7–8, HCSB).
The point is, we can ask questions of God sinfully, thinly veiled queries which are really asking Him to justify Himself. We can ask questions sinfully like the Pharisees did, just to gather evidence that God is not worthy. Or we can be a Mary or Habakkuk and sincerely ask and give him worshipful praise when the answer comes- or not, as Job did.
All the articles linked to here are good to explore the question of whether it is OK to question God. Ultimately though, Mary’s and Job’s conclusion, “Let it be done to your servant as you will,” and “Shall we actually accept good from God but not accept adversity?” is the best thought to rest on as you await an answer- whether it comes or not.