“Who chose which books would be in the Bible?” This is a common question, and sometimes people make the claim that the decision was made by people who had an agenda to push: they chose those books that they liked, and rejected the ones that didn't support their ideas. The idea has many problems, first of which is that it is based off of a conjecture rather than on any real information. What are the historical sources that a person would go to in order to support this claim? I have yet to really see anything other than the insistence that "this is probably what happened." Along with this, it is assuming that the leaders of the church were not sincere in their faith and devotion--they were just trying to push their own agenda. And to be fair, it is hard to fault this suspicion, because history is indeed sadly filled with people who have used the church, and even the scriptures, as tools and weapons to further their own ends. But, again, this would need more substantiation than just the fact that someone else did it at some other point in time. Thirdly, such an idea is arbitrary, because it showing very little knowledge of the true history of the book which we now call the Bible. I remember one time when I was explaining to a coworker about a class in seminary in which we had discussed the history of the canon of the scriptures. They, assuming that any genuine look in history would show the Bible as a fraud, asked whether this hurt my faith. I was somewhat taken aback by this. "Hurt my faith??" I said "No, it strengthened my love for and trust in the Scriptures."

Another assumption that is behind the statement that men "chose" the books that they wanted to be in the Bible is that the they made their choice out of a pool of writings that all had the same equal potential to “become” scripture. Basically, The Revelation of John and the Revelation of Peter went to an audition, and they chose John over Peter; "Sorry pal, he just did a better job." This is, yet again, another assumption that shows a lack of genuine knowledge on the subject. It is true that there are other ancient writings which claimed to have been written by various Biblical figures, such as the Gospel of Thomas, or 2 Ezra, yet these books were not included for much more important reasons than “the men made the Bible didn’t like what they said so they left them out.”
Those books that were left out of the list of Scriptures of the New Testament because they saw them and they recognized them as frauds. They knew that they had not been given to the church through the ministry of the Apostles—those men whom Jesus commissioned to be His authoritative witnesses to the world concerning the news of the resurrected Christ (Acts 1:8). Consider the words of Athanasius,  a church leader in the 300s A.D.:

“But while the former are included in the canon and the latter are read, no mention is to be made of the apocryphal works. They are the invention of heretics, who write according to their own will, and gratuitously assign and add to them dates so that, offering them as ancient writings, they may have an excuse for leading the simple astray.” -39th Festal Letter, AD 367.

Note what he says: “They write according to their own will.” This means that they are writing according to what fancies them, and not according to what Christ has taught or commanded. These later books were also rejected for their content: content that did not align with the teachings of the Old Testament, with the teachings of Jesus, nor those writings of His Apostles that had already been received.

Now why are Christians to be so concerned for this? Why did Athanasius, for example, have such strong words regarding the books called apocrypha (literally: hidden away)? The Scriptures are called God’s Word because, as the Apostle Paul says, they are “breaded out by God” (θεόπνευστος; see 2 Tim. 3:16). Therefore these writings bear the full weight of God’s authority. It is God who speaks to His church in and through the Scriptures He has given us. This means that to try to claim something as scripture that was not given by God is to be an imposter. Impersonating an officer of the law is very illegal in our country, because such a person has not really been sanctioned to hold and exercise any legal authority. So when someone claims to speak for God, offering their own words as God's words, they are at least impersonating a prophet or apostle--they have not been commissioned by God to speak on His behalf. At the worst, they are actually attempting to impersonate God Himself and will have to answer for that before Him one day.

The Christian is to receive the Word of God because they hear the voice of their God and Savior there, and for no other reason. If I label something as the Word of God because it fits some agenda of mine, who am I really treating as God? Is it the true God who speaks in and through His Word, or am I elevating my heart to a place of authority. As Augustine once said: "If you believe what you like in the Gospel, and reject what you don't like, it is not the Gospel you believe, but yourself." Similarly, if I accept the Bible as scripture simply because someone told me it is--like the church or a pastor--without hearing and seeking the voice of God therein, who is really the voice of authority in my life? It ends up being the testimony of man, doesn't it? This is why the idea that the church "decides" what is scripture and what isn't just false, but dangerous; it removed Christ from His place as the only head of the church, and gives that position to the church itself--or at least to those who have positions of leadership in a given church. The reformers fought against this by emphasizing that "scripture alone" is the authority of the church, because it is the Word of God, and being thus, is to be accepted for the very reason that it comes from our God, the sovereign creator of all things, whose voice it is our obligation and our joy to listen to and obey.