Why is Mary the Mother of the Church?
The Church is the Mystical Body of Christ; we are its members, and He is its head (cf. Romans 12:4; I Corinthians 12:12; Ephesians 1:22-23; 5:23; Colossians 1:18). By the mere fact that the Church is a living, breathing divine organism, and that a mother cannot give birth to a head without giving birth to the whole body, Mary is the Mother of the Church.
Since these words were intended universally, John was representing the Church while Mary was who she is—the Mother of God. It was at this moment that our Savior gave His mother as the Mother of the Church.
"When Jesus saw his mother, and the disciple whom he loved standing near, he said to his mother, 'Woman, behold your son!' Then he said to the disciple, 'Behold your mother!'" (John 19:26-28).