I think it is because men are believed to be the head of the family. So a family tends to use the father's name in order to identify themselves to the community. I do not think it is a bad idea, since it shows respect.
Actually we have it all wrong in my opinion. The mother is the undisputed family of every child. Doing genealogy is a pain finding women after marriage. In Spain they use the mother's name first, followed by the father's name. If you think about this, it really makes sense and honors both parents as well.