I can't believe there is even an argument here...
SRD said:An attack roll represents your attempt to strike your opponent on your turn in a round. When you make an attack roll, you roll a d20 and add your attack bonus. (Other modifiers may also apply to this roll.) If your result equals or beats the target’s Armor Class, you hit and deal damage.
It doesn't matter whether your weapon deals damage or not. If your attack roll equals or exceeds your target's AC, they take 1d6 fire damage--even if it was a +1 Flaming Cotton Ball. The argument that a weapon must deal its own damage to deal the fire damage might be a reasonable houserule, but it's clearly not the way it works in the RAW.SRD said:Upon command, a flaming weapon is sheathed in fire. The fire does not harm the wielder. The effect remains until another command is given. A flaming weapon deals an extra 1d6 points of fire damage on a successful hit. Bows, crossbows, and slings so crafted bestow the fire energy upon their ammunition.