I'll keep this short and sweet. This is my confusion.
Masterwork
A masterwork weapon is a finely crafted version of a normal weapon. Wielding it provides a +1 enhancement bonus on attack rolls.
Special Weapon Abilities
Some magic weapons have special abilities. Special abilities count as additional bonuses for determining the market value of the item, but do not modify attack or damage bonuses (except where specifically noted). A single weapon cannot have a modified bonus (enhancement bonus plus special ability bonus equivalents, including from character abilities and spells) higher than +10. A weapon with a special ability must also have at least a +1 enhancement bonus. Weapons cannot possess the same special ability more than once.
So let's give the example of flaming. I want to add flaming onto my longsword. I look at the requirements: A weapon with a special ability must also have at least a +1 enhancement bonus.
Ok, I look at my Masterwork longsword and see: A masterwork weapon is a finely crafted version of a normal weapon. Wielding it provides a +1 enhancement bonus on attack rolls.
Then I'd pay the 2,000 Gp for the special ability?
I've asked this question to one of my other friends but he says you need a +1 from the enchantment that costs 2,000 Gp then you can add the flaming for another 6,000 Gp for a total of 8,000 Gp. But why is that? Does Masterwork not cover the prereq for the weapon special ability?
Fair point of confusion.
A masterwork weapon provides a +1 enhancement bonus to attack rolls.
A +1 magic weapon provides a +1 enhancement bonus to the weapon.
The bit that's not clearly explained is that a +1 enhancement bonus on a weapon affects both attack and damage rolls, thus the masterwork benefit is insufficient to meet the requirement. Your friend is right.
Short answer, your friend is correct.
All magic weapons must be masterwork, so calling out the required enhancement bonus is redundant in your reading.
This is supported by the lack of any weapons with a special ability and no generic plus in publisged material and is the "common knowledge" among every table I know of, but now that I try to justify it in writing, I can't find a concrete statement to quote, interesting.
Thank you both for letting me now this, but where exactly does it say all of this? It seems like this is 'Common Knowledge' as Java Man said but there is no actual writing that states this.
The writing is in how it is parsed. It is basically, are you referencing the name "enhancement bonus" or are you referencing a result "enhancement bonus". In this case, the result "enhancement bonus" is a result of the Masterwork property while the magic weapon enhancement bonus is a named thing.
Masterwork provides a +1 enhancement bonus to attacks. Ie., it does not provide a general enhancement bonus.
However, the +1 magic weapon enhancement bonus is an enhancement bonus that provides a bonus to both attack and damage rolls.
A magic weapon is enhanced to strike more truly and deliver more damage. Magic weapons have enhancement bonuses ranging from +1 to +5. They apply these bonuses to both attack and damage rolls when used in combat. All magic weapons are also masterwork weapons, but their masterwork bonuses on attack rolls do not stack with their enhancement bonuses on attack rolls.
Basically, if you just read the section on the Masterwork property you get confused. If you read the magic section it becomes clear that the magic section is referencing the the magic bonus on a weapon.
Edit: Back in 3.5 there was an example that stated you could not have a Keen Rapier but it must be a +1 Keen Rapier. Pathfinder generally does not include examples and this probably results in a lot of confusion.