In the sixth chapter of the Gospel of John, it details the events of Jesus feeding the 5,000 disciples (in which only the men were counted, but also included women and children, which means that the crowd could have easily been closer to 10,000). This famous miracle made Jesus very popular, and the very next day he did something extremely controversial by stating that his disciples would have to eat his flesh and drink his blood. This was a direct contradiction to the Law of Moses, and most of his disciples left him, and understandably so. Even his Apostles were questioning themselves, but they had seen too many miracles, and their faith had been confirmed to many times to turn back now. Verses 67-69 state that Jesus said to his Apostles "Will ye also go away?" and Peter answered "Lord, to whom shall we go? Thou hast the words of eternal life, and we believe and are sure that thou art that Christ, the Son of the living God."
Why did Jesus do give such a controversial sermon advocating cannibalism? We learn in verse 26 that this massive crowd wasn't there for Jesus's teaching, but for free food. Jesus rebuked the people by saying that they were only following him because they ate the loaves and were filled the previous day. Jesus desires quality over quantity, and has no use for false disciples that want to follow him for the wrong reasons. What does Jesus desire? Again, that's answered in John 6, verses 28 and 29. A spokesman for the false disciples asked Jesus what they needed to do to please God (and maybe score some food), and Jesus told them that they needed to believe on "him whom he hath sent" (i.e. have faith in Jesus).
These false disciples can be identified by characteristics that are all too common in the church today, first of which is the desire for blessings or material prosperity. This can be understood as the belief that God will bless you and keep bad things from happening to you if you keep the commandments, go to church, tithe, read your scriptures regularly, etc. The problem with this mindset is although it is true that God loves us, and that he desires to bless us, there is only a general cause and effect between behavior and blessings. It is true that sin can cause judgment, and piety can lead to God blessing you, but that's not a money back guarantee.
Just think of the Apostles themselves, or the list of prophets in the Old Testament who suffered and died in horrible ways all while following God. Why did God let these just and faithful men suffer and die if keeping the commandments always leads to blessings? Some people try to have it both ways, and say something to the effect that although God allows bad things to happen to you, he'll always help you overcome it in the end and bless you. They might point to Job as an example of this, but that ignores the counter-examples of the apostles and prophets that were martyred to death, and received no relief from their suffering during their lives at all.
The real tragedy of this mindset is that people lose their faith when "bad things happen to good people". How many people have left their church or become atheist because they experienced personal tragedy? The worst part is that although the initial "prosperity preachers" meet success, people eventually leave the church when they see their lives not improving, and then their hearts are hardened to real missionaries trying to share the true Gospel.
The other characteristic of this group of false disciples is a reliance on human reason over faith. These people were pious Jews. We know this because they (or at least their spokesman) said that their fathers ate manna in the desert. This was referring to the Exodus of Moses, when the children of Israel ate manna while living in the desert for 40-years.
God doesn't desire disciples who view their belief in God as an academic exercise. For example, there is something called "Pascal's Wager" from a 17th-century Apologist who stated that God either exists or doesn't, but if you believe in God you either gain everything (if he exists) or lose nothing (if he doesn't exist). Likewise, if there is no God, you gain or lose nothing either way. Pascal's wager proves the logic behind academic faith, which I'm defining as someone who believes in God only because it's the most logical option, or simply because they are "playing the odds" as Pascal suggests.
God doesn't want people to follow him just because it seems like a good idea, or because they haven't found a theory to disprove him yet. Atheist "scientists" are always trying to come up with new ways to disprove God, so at any rate, people are going to find a convenient theory sooner or later, and leave the church regardless.
Remember that God wants quality over quantity. He would much rather have small tight-knit and faithful churches than massive mega-churches full of "fair-weather" Christians. Sometimes God does things that test us in order to separate the true Christians from the groups I've detailed above. When God does something like this, only the disciples with true faith will stay, much like Peter and the Apostles stayed. They knew Jesus personally, and didn't forsake him even after such a controversial sermon.
So what am I trying to say? I'm not saying that you should not question things, but what I'm saying that there are times when your faith will be tested by either tragedy or human reason. If you do not have real faith, you will become discouraged when tested if your faith is based on either God blessing you for keeping the commandments, or based on apologetic arguments.
Just like the crowds in John 6, we are only asked to believe (i.e. have faith) in Jesus Christ, no more and no less. If we view God as some kind of celestial Santa Claus, or have replaced faith with reason, then God will sift us out of his church sooner or later. This isn't to say that God doesn't bless his children, or that Christian apologetic doesn't have a useful purpose. I'm just saying that it's not a replacement for true faith, and God obviously agrees according to John 6.