Paul refers to himself as the father of the Corinthians, and Timothy, in a spiritual way, since he brought them the Gospel of Jesus Christ and in some way was responsible for their rebirth. (cf. 1 Corinthians 4:14-17) so, in a similar manner, we acknowledge the fatherhood of all those who were ordained to preach the word and bring us the Eucharistic food.
It is an ancient tradition and in no way contradicts what Jesus said in Matthew 23:9, call no man your Father. The Scriptures would not contradict themselves, nor would Paul misuse this title.
What Jesus was condemning is the notion that someone can look to anyone but himself as the Way and Source of Life. In ancient times, as is true today, too often people would look to some individual as an enlightened one, who had a way of salvation or enlightenment. These are like Gurus, new age masters, and others who presume to be equal to or above Christ. There is no other way but through Christ. (cf. Acts 4:12)
All priests, as sharers of the Apostolic ministry, share in the teaching and preaching of Christ and do not claim a different way; therefore the title father, is a familiar term, meaning belonging to the family. Nuns of a leadership position are called mother, because all of our roles belong to the Family of God of which we are all children. Likewise, we have the titles brother and sister.