Can anyone explain to me how the combat masteries work? I know that it says that it increases damage, but what damage does it actually increase? Is it just the physical damage, or is it the total damage of the weapon (physical and any elemental)?
This might seem counterintuitive, but elemental damage on weapons isn't part of "the total damage of the weapon." It's an on-hit effect that is applied separately, not part of the calculation determining the damage of the weapon. The base damage of the weapon is modified by % Damage effects like the barbarian's weapon mastery skills.
Those skills also enhance Attack Rating (chance to hit) and give a % chance of Critical Strike (doubles damage).