It was not long ago that the majority of Americans were expected to be in church on a Sunday morning. Children went to Sunday School and learned their Bible stories. God's word was accepted as true, no questions asked. Those days are over--for the most part.
There are still children who are brought to church by their parents. They still go to Sunday School and learn their Bible stories. They accept God's word as true, and they don't question it. They believe their parents would not enforce lies upon them, and they believe their church is not out to deceive them.
This is not a flawed system. The church is not lying to people about the Bible, and children's parents are not out to deceive them. We are doing exactly what our Lord has instructed his people to do: to pass along the faith to the next generation (cf. Psalm 78, among many other Scripture references). We proclaim, "This is what the Lord says," and therefore declare it to be true. We do not spend time talking about other religions or other world views when children are at young age. For one, we want to use our time to teach what is true, not what is false. For another reason, young children are not ready to grapple with the difficulties of such differences. Just as we don't start discussing varying political ideologies with 1st graders, so we don't do studies on comparative religions in Sunday School.
Things change, however, as people get older. They get exposed to different ideas. These ideas include challenges to the Bible, to the claims of Jesus, to the Christian faith, and so on. It is entirely likely that the children who were brought to church and Sunday School by their parents hear these challenges for the first time when they are teenagers or college students. But the questions can really nag at a person, especially when it seems like a valid question. (You know what? If often is a valid question!) Challenges are often simply assertions made against the Christian faith--insisting that the Bible makes claims it doesn't make (that a loving God would never allow evil), or doesn't make claims it does (e.g., that Jesus is God). And since the young Christian does not have an immediate answer for these challenges, they may assume that there are no answers for these challenges. As a result, they drift from the faith, refusing to be duped any longer by these alleged lies.
Such challenges and questions can be shocking. At first, the young Christians probably simply dismiss these questions and challenges because they refuse to believe that their parents and their church were lying to them all those years. Or, they do not want to believe that they were so easily duped. But, chances are, the questions will haunt them. What about those challenges? How do I know that I have believed the truth? Can anyone really know the truth?
Once those questions begin, they will demand answers. At this point, there are not really any problems. The questions should be answered. The problem begins not when the Christian begins to seek answers, but when that Christian goes to all kinds of sources but the Bible and/or their pastor to get some solid answers. Once again, the Church is not out to lie or deceive. That is the devil's work, and he is really good at it.
To the young Christian who is confused, whose faith is challenged, who has questions, and so on, take heed! You are not the first person to have struggled with this. You are not the only one whose faith has been challenged, who has had doubts, or who is yearning for better answers than you learned in Sunday School. And just because these questions and challenges are new to you, they have certainly been grappled with before, and they even have been answered. Let it be said again: The Church is not out to lie or deceive. That is the devil's work, and he is really good at it. The devil delights in seducing you away from the faith, and he will use your own quest for truth (and often your air of superior knowledge when you have "seen through the lies" in undermining the Bible) to entice you away from Jesus.
So, what can you do? The answer is not to ignore the Bible, Jesus, the Church, or your pastor. These are always here to serve you, to encourage you, to strengthen you, to comfort you, and if you are drift away--to warn you. The Bible is proven itself reliable against all attacks. Centuries of Christians have learned this (although many have been deceived away from it, too). God does not lie. His word will not fail you. It still stands to this day, and it will endure forever. Those who take their stand on it will live forever too. These are the words of eternal life, and you will not find that anywhere else.
If you have questions or want to know how to respond to challenges, speak to your parents and/or your pastor. They have been given to you for your benefit. Neither your parents nor your Church are out to lie or to deceive you. They pray for you. They love you. They seek your eternal well-being. And that is why they encourage you to be at church and point you to Jesus.