Traditionally, Saint John has been identified as the author of the fourth gospel. He has also been identified, within that gospel, as one of the twelve apostles, the one “whom Jesus loved” (Jn 20:2).
The phrase is not meant to suggest that any of the eleven apostles (or anyone) is not loved by Jesus, for Jesus says numerous times that he loves the others (and all those to whom they will minister). It may be that the author wanted to remain anonymous out of a sense of humility. Perhaps too the phrase is meant to serve as a way of seeing the disciple (even every disciple) from Jesus’ perspective.
Love is a dominant theme in the gospel according to John. It focuses on Jesus’ love for the world and his call to everyone to respond in kind: “This is my commandment: love one another as I love you. No one has greater love than this, to lay down one’s life for one’s friends” (Jn 15:12-13).