The short answer is no, it is not wrong to question God if you are coming from an honest place.
There are several verses in the Bible that lead people to believe that we are predestined by God to believe or not believe His Word. Some Bible preachers use these verses to teach that whatever is happening in our lives is by God’s design and God’s will, therefore we should never question it.
Romans 8:29,30 For whom he did foreknow, he also did predestinate to be conformed to the image of his Son, that he might be the firstborn among many brethren. Moreover whom he did predestinate, them he also called: and whom he called, them he also justified: and whom he justified, them he also glorified.
Ephesians 1:4 According as he hath chosen us in him before the foundation of the world, that we should be holy and without blame before him in love:
True Calvinist’s believe in double predestination, meaning some people are chosen for salvation and some are chosen for hell. They believe that God is in control, picking and choosing, predetermining and micromanaging the world for His, eventually to be understood, will and plan. Some Preachers even believe and teach that God chooses some people to be saints and others to be their Judas. In believing God is up there like Zeus and the other Greek gods pulling strings and interfering in the lives of mortal man, either for their good or for their destruction, they oddly gain the comfort and strength needed to accept horrible and painful events as being God’s will in their lives.
You hear, “God has a plan, Brother. It is not our place to question why.” “God loves you, so he is testing you.” God knew you could handle it, so He gave you …” “Take it by faith, Sister, God is in control.”
But are those exhortations true?
I don’t think so. I believe every one of those statements are lies, and that if we believe them we will never have the freedom to which God called us. If we believe them it will be said of us as it was said of the children of Israel, “My people are destroyed for lack of knowledge.” (Hosea 4:6)
You see, God wants His people to trust Him and take Him at His Word. He wants us to rise above. God wants us to know the truth. He doesn’t want us to take it by faith and not ask questions. He wants us to think and question and come unto the knowledge of the truth. (1Timothy 2:4)
A simple overview of the Gospels shows that Jesus Christ welcomed questions. He also asked them.
Luke 2:46 And it came to pass, that after three days they found him in the temple, sitting in the midst of the doctors, both hearing them, and asking them questions.
Jesus Christ stopped asking questions of the religious leaders only after he came unto the knowledge of the truth by studying the scrolls thoughtfully in prayer to God. Even after he stopped asking questions of the religious leaders, he continued asking questions of God.
Paul was not opposed to questions either.
Act 17:2 And Paul, as his manner was, went in unto them, and three sabbath days reasoned with them out of the scriptures,
All through the Gospels, and the Epistles, you see people asking questions. The only time issue was taken with them was when the questions were being asked from an arrogant, self-righteous, destructive place. Questions and answers, like everything else in life, are a heart thing.
Titus 3:9 But avoid foolish questions, and genealogies, and contentions, and strivings about the law; for they are unprofitable and vain.
Honest questions are a thing to embrace. And think about it, many people turned to God only after they asked the question, “Isn’t there more to life than this?”
God never wants us to take anything by faith or allow someone else to determine what are our beliefs are in Him. God wants us to search the scriptures daily to see if what we are taught is truth.
Act 17:11 These were more noble than those in Thessalonica, in that they received the word with all readiness of mind, and searched the scriptures daily, whether those things were so.
But the Devil doesn’t want that for us. Not only does he not like honest questions, he wants people to believe God is responsible for all the bad, not necessarily the good, but certainly the ugly things that happen in our lives and the world. The Devil knows that if people believe God is responsible when a tragedy happens, it takes the pressure off of him so he can work his madness without interference. These people who believe God is responsible for everything somehow feel better about the tragedy and it becomes easier to digest. “God is in control.” Sadly, the people watching ask, “Why would you believe in a god like that?”
The micromanaging, picking and choosing, God of Churchianity is a lie. 1 John 2:21 says no lie is of the truth. 1 John 1:5 says, “This then is the message which we have heard of him, and declare unto you, that God is light, and in him is no darkness at all.”
God’s will for us?
John 8:32 And ye shall know the truth, and the truth shall make you free.
Ask questions. Study the Word. If you are going to take it by faith, make sure that faith is the faith of Jesus Christ and not your own.