Among all of the Bible's teachings, the instruction given in John 3 regarding being born again is perhaps the most liable to being misunderstood. In fact, as soon as it was out of Jesus' mouth, Nicodemus misconstrued His meaning, taking Christ's spiritual symbolism literally and physically. Ever since, people have stumbled over various parts of Jesus' teaching in this passage, and usually the stumblingblock is the imagery.
To convey essential, spiritual principles, Jesus uses imagery extensively in the gospels, and perhaps the most in the book of John. Along with John 3's imagery of the new birth, the book contains many references to light, water, bread, blood, blindness, sheep and shepherds, fruit, seed, vines, and several others. In nearly every case, they have spiritual meanings that transcend a plain, literal sense.
The book of John also contains a remarkable witness to the fact that Jesus was constantly being misunderstood. An example appears in nearly every early chapter and continues sporadically to its end. Even in the last chapter, Jesus has to tell Peter three times to feed His sheep before the apostle realizes that His Master is teaching him that he could demonstrate his love for Him by truly caring for His people for the rest of his life.
John W. Ritenbaugh
Born Again or Begotten? (Part Three)