I've seen a lot of people confuse the two. % weapon damage and bonus damage are two totally different parts of the damage equations. I don't know the damage equations, I just know these two things are separate. Allow me to elaborate.
Max yellow runed Weapon Throw with max Fury does 1290% weapon damage. If our weapon damage is 1, we do 12.90 damage with Weapon Throw. This is our skill's base damage - 1290% weapon damage.
If we then apply a Battle Rage with max red rune, we are given a 100% damage bonus. Well our damage is 12.9 with a 1 weapon damage, so 12.9 + (12.9 * 1.00) = 25.8 damage.
I've read people say this is incorrect and it should just be 1390% weapon damage or 13.9 damage. This logic is flawed. Battle Rage, and bonus modifiers like it, do not say "increase skills that use weapon damage as a factor by an additional 100% weapon damage". It says "increase damage by 100%".
If my skill hits for X, a damage modifier of 100% would make my skill hit for 2X, not some convoluted formula to try and go back to see how the skill applied it's damage, then see if it is based off of weapon damage, and then increase that number by a factor of 1.
Furthermore, a passive that increases the damage of a skill by X% is not the same as increases your skills damage based off of weapon damage by another X%, else it would read "when you use skill X, increase damage by an additional 100% weapon damage." But it doesn't read that way, it says "increase the damage of skill by 100%". This should mean the passive is more along the lines of Battle Rage as far as how it should apply it's bonus.
Max Fury Weapon Throw with max yellow rune at 1 weapon damage (MFWT) = 12.9 damage.