'Doubting Thomas' has got a bad name from people because he wouldn't believe Jesus had risen from the dead until he had seen Him. But, on the other hand, those who will believe everything without checking are called 'gullible'. We appreciate the example of the Bereans who checked out the preaching of Paul the apostle with scripture before accepting it (Ac.17:10,11). Jesus rebuked His disciples for doubting instead of believing (Lk.24:38). Where is the balance?
Doubts about various things is one reason why people fall away from the faith. We may also be perplexed at times with different questions in our mind – why a loving and almighty God allows evil to rule, how a loving God can send people to hell, why God is not answering our prayers, what can we do about problems we find in the Bible, etc. We can mostly find satisfactory answers to doubts if we would consult with godly people or read their writings. But if we brood over our doubts without seeking help, we may even enter into a situation where deceiving spirits find it easy to inject our mind with the idea that God cannot be trusted, or that He doesn't exist. God warns us that before the day of the Lord there will be a great apostasy (falling away) (2Th.2:3).
God has not arranged things in such a way that all our doubts can be cleared, because there are many things He has not revealed to us. There will be always questions left, and always things that our small minds cannot explain or understand. So, if our relationship with God is going to depend on understanding everything about Him, we will fall away at some time. There are some others who try to escape from this problem by not allowing themselves to think about such issues altogether. That will not work for all the time because occasions will come in life for everyone when we need some answers.
Ultimately we have to come to the place where we are comfortable even when knowing very well that there are things we don't understand. Our life has to move from living based on facts we can explain to living by faith in God as a Person whom we know personally. Of course, our faith in Him is based on facts we know about Him, but it is also based on the confidence we have developed in Him that has come through personal experience with Him. It is only then that we can survive doubts that come to us from time to time. We can then draw upon our 'Ebenezer' of knowledge that says, "So far God has kept me, and I can depend on Him to take care of me even in the future" (1Sa.7:12).
This doesn't mean that we stop looking for answers. The more clearly we see the answers, the more quickly we can put away the doubts that come up in our mind. We also become able then to help others around us who are struggling with doubts.
On the final day we are not going to be examined regarding our knowledge, but on how close we have come to Jesus. Cleverer ones can deal with apologetics, but even the least of the saints can get to know God (He.8:11).