"For God so loved the world that he gave his one and only Son, that whoever believes in him shall not perish but have eternal life. For God did not send his Son into the world to condemn the world, but to save the world through him" (John 3:16-17).
There is a certain church that I pass on my way home from work every day. Like most churches, this church has a sign out by the road. I have already expressed my extreme frustration with church signs elsewhere, so it should come as no surprise that I am always keeping my eyes open for the latest and greatest "saying" adorning local signs. The particular church has had this message up for the last several weeks: "Christianity is not a religion." Below this, the sign instructs readers to read John 3:16-17 to find out why.
Being quite familiar with John 3:16-17, I was a bit puzzled as to why these two verses from the Gospel of John prove that Christianity is not a religion. While I am certainly aware of what the church is trying to say with its sign-message (viz., Christianity is not a religion, it is a relationship with Jesus), I am confused as to how John 3:16-17 proves its point. If anything, these verses reinforce the fact that Christianity IS a religion. Christianity cannot be proven empirically, i.e. by using the scientific method or our five senses. When Thomas claimed that he would not believe that Jesus actually rose from the grave unless he could see and feel where the crucifixion nails had been (John 20:24-29), he was making an empirical demand. Thomas wanted proof that Jesus was alive; the testimony of the other disciples was not enough for him. When Jesus appears and grants Thomas his empirical proof, Thomas exclaims, "My Lord and my God." Jesus’ response is as chilling as it is brief: "Because you have seen me, have you believed? Blessed are they who did not see and yet believed."
Earlier in his Gospel, John tells of a similar event transpiring between Jesus and Nathanael. Having already become a follower of Jesus, Philip goes to Nathanael and tells him that he has found the Messiah—"Him of whom Moses in the Law and also the Prophets wrote" (John 1:45). Nathanael is skeptical so Philip invites him to "come and see." When Jesus tells Nathanael that He saw him "under the fig tree," before Philip called him, Nathanael believes and exclaims: "Rabbi, You are the Son of God; You are the King of Israel." In much the same way as He responded to Thomas, Jesus answers: "Because I said to you that I saw you under the fig tree, do you believe? You will see greater things than these" (John 1:50). Thomas and Nathanael both "saw and believed," but Jesus questions each man’s empirically-based belief. While our modern society tells us that "seeing is believing," Jesus tells us that "believing is seeing." He chides both Nathanael and Thomas for having such a shallow view of believing; one believes because Jesus tells him that he was under a tree and the other because he was able to touch Jesus’ nail-scarred hands. Jesus knows that belief that is so easily attained is also easily lost. He warns Nathanael and Thomas that a faith of seeing—of empirical verification—is really not a faith at all and can easily miss the greater blessing that awaits them.
In the book Exploring Theology, Robert Morgan writes this:
The body of evidence for the truth of Christianity is staggering, and I believe the truth of Christianity can be established to a 99 percent level of certainty. The remaining 1 percent is the step of faith you take when you "confess with your mouth, ‘Jesus is Lord,’ and believe in your heart that God raised him from the dead" (Rom. 10:9). 
Morgan’s view of faith is pretty standard in modern evangelicalism. Most Protestant Christians would agree with Morgan’s "99 percent level of certainty," although I would guess that most wouldn’t put it quite that high—maybe more of a 75-80 percent level. In fact, my estimate is probably too generous. A 2008 Pew study revealed that 47% of evangelicals believe that other religions can lead to eternal life. This is down (in a good way) from 57% in 2002.  According to this study, nearly half of American evangelicals are not entirely convinced (or even 99% certain) that Christianity is true in all of its claims and doctrines.
The problem that lies behind Morgan’s 99 percent level of certainty and the church sign’s proclamation that "Christianity is not a religion," is a misunderstanding of what constitutes "religion." Most people have an idea that religion only deals with the things of God. R.C. Sproul defines the belief of most when he writes:
Intellectual assent involves the assurance or conviction that a certain proposition is true. When we say that we believe that George Washington was the first president of the United States, we mean that we affirm the truth of that proposition. This is not faith of a religious sort, but it is integral to a person’s belief-system concerning real states of affairs. 
Sproul makes the claim that believing that George Washington was the first president is not a religious belief. In other words, Sproul is making the point that believing the historical fact that Washington was the first president is not the same as believing the historical fact that Jesus is the Messiah. One is a historical "proposition," while the other is a "religious" commitment. Sproul seems to believe, like most evangelicals, that because believing that George Washington was the first president has no bearing on your eternal destiny, it does not fall into the realm of "religion." But this is somewhat misleading. While it is true that mere intellectual assent to the historical fact of Jesus being the Messiah doesn’t make one a Christian (after all, even the demons believe; James 2:18-19), believing that Jesus is the Messiah is just as much a faith commitment as believing that Washington was the first president. Both involve believing something to be true that we can’t directly experience or verify to be true. The fact that most people believe that George Washington was the first president doesn’t make it true, any more than most people disbelieving that Jesus is the Messiah makes it false. Truth is not determined by a majority vote; even if the majority is 99 percent.
Religion does not only deal with where you will spend eternity. Every person on the planet has a religion (in fact several of them), whether they realize it or not. When a woman makes a decision to have an abortion because she believes that it is only a "clump of cells," she is making a religious decision. When a man chooses to euthanize his aging and decrepit father because of his low "quality of life," he is making a religious decision. When two parents decide to work longer hours and make more money to put their child through college, they are making a religious decision. Any time we act on our beliefs—e.g., fetuses are not babies, quality over quantity of life, better education means a better job, etc.—we are acting out of religious (i.e. spiritual, not empirical) convictions, even if those beliefs have been shown to be 99 percent capable of predicting future events (which begs the question of cause and effect, but we’ll save that for another day!).
What do we mean by the word ‘religion’? It is "the binding tendency in every man to dedicate himself with his whole heart to the true God or an idol," according to F. Nigel Lee. In this sense all men are religious because no man can escape being a man in the image of God created to worship and serve God, rebellious and unregenerate though he be. Romans 1:25 says, "For they [mankind] exchanged the truth of God for a lie, and worshipped and served the creature rather than the Creator…" Man is inescapably religious. 
In other words, to make the claim that Christianity is not a religion flies in the face of Romans 1 (and other passages), where the Bible makes the point that God is to believed for the sole reason that He is God. Yes, Christianity is a relationship, I am not denying that. But as Brian pointed out yesterday, relationships fail all the time because people go into them with false expectations. Saying that Christianity is a relationship doesn’t magically take it out of the "religious" realm. The Bible is filled with individuals who desired a relationship with God, but wanted it on their own terms. They had one idea of what a relationship with the Holy God would mean, but God had another. Like the rich young ruler, these people "go away grieving" (Matthew 19:16-26).
Paul writes that unregenerate men exchange the "invisible" truth of God for something that is visible: the creation. They worship the creation, rather than the Creator. Man is not to judge God by the things He has made, they are to submit and believe His truth because of what He has made. "Do not fear those who kill the body but are unable to kill the soul; but rather fear Him who is able to destroy both soul and body in hell" (Matthew 10:28). When the claim is made that Christianity is not a religion, what is really being said is that Christianity is "provable" in some sense. Abraham’s answer to the rich man in Luke 16 puts this idea to rest fairly quickly: "If they do not listen to Moses and the Prophets, they will not be persuaded, even if someone rises from the dead" (Luke 16:31).
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Although Robert Morgan is free to make the assessment that the truth of Christianity can be established to a 99% level of certainty, what he is really saying is that he is personally 99% certain of the truth of Christianity. Even if it were possible to convince the world of the 99%, we would still be faced with that pesky 1% that requires faith. In fact, it is the 1% that makes the other 99% relevant. Proverbs 1:7 states emphatically: "The fear of the Lord is the beginning of knowledge." That is, we cannot know anything truly without first believing. "Without faith it is impossible to please Him, for he who comes to God must believe that He is and that He is a rewarder of those who seek Him" (Hebrews 11:6). "Only one of the world’s religions is TRUE and from God, and that is the religion of Christianity, founded on the Spirit-inspired writings of the apostles and prophets in the Bible." 
All truth—"true truth" as Francis Schaeffer called it—originates with the God of Truth, He who is the Definer of reality, He who calls light out of darkness and apart from Whom nothing was made (John 1:1-5). Apart from this God of truth, we can do nothing (John 15:5), and this includes determining something to be either 99% true or 99% false. John the Baptist stated it simply enough: "A man can receive nothing unless it has been given him from heaven" (John 3:27). Or as Saint Anselm put it in the 11th century: "I do not seek to understand in order to believe, rather I believe in order to understand." The religion of Christianity precedes the relationship with Christ, just as marriage vows precede the marriage.
 Robert J. Morgan, "Evidence and Truth," Exploring Theology: A Guide for Systematic Theology and Apologetics (Wheaton, IL: Crossway,  2007), 221.
 John R. Franke, "Still the Way, the Truth, and the Life," Christianity Today (Dec. 2009), 30.
 R.C. Sproul, Faith Alone: An Evangelical Doctrine of Justification (Grand Rapids, MI: Baker Book House, 1995), 96-97.
 Joseph C. Morecraft III, "The Counterproductivity of Not Linking Christianity and Politics," The Theology of Christian Resistance (Tyler, TX: Geneva Divinity School Press, 1983), 151.
 From the forthcoming 5-volume commentary on the Westminster Larger Catechism by Dr. Joseph Morecraft, Authentic Christianity (Powder Springs, GA: American Vision), 2:493.