It means that that person actually runs the house. Wife or husband but generally speaking, it means the wife. I guess the Mods do wear the pants here but they have bosses too. So I don't think they wear the pants, they just keep the site clean and proper.
He or she who wears the pants in the house is the one in control. I had a friend who once said, "I wear the pants in my house--just don't tell my wife!" :) Of course, we laughed at him--hey, try not to wrestle for control. You would be much happier if you can get along with the others! :)