We, as Catholics, call the Pope Holy Father not because we consider him to be "holy" but because the office he holds is considered to be installed by Christ himself. Therefore, the office the Pope occupies is Holy. Hence, since as a servant of the church, he is our father, in Christ, and since the office he holds is Holy, in Christ, we refer to him as "Holy Father."
Again, Catholics do not consider the Pope himself to be holy, but the office he occupies is. See my hubs. Founded by Christ parts I, II, and III for a more detailed answer.
Hope this helps.