I don't know of any such rule. The closest thing I am aware of would be the special Rock Throwing ability that giants get, which give them a greater range when specifically throwing rocks.
It would be a reasonable house rule to increase throwing range for large creatures, but I'm not sure exactly how I'd approach the numbers.
Rock Hurling: "The size of the range increment varies with the creature."
Hill Giant Entry: "Special Attacks rock throwing (120 ft.)" - Which basically means the base range for a Hill Giant's throw (1 range increment) is 120 feet. That's a tad better than 10'.
So if it says it, it gets it. If it doesn't (Storm Giant) it doesn't. Some Giants just aren't good with throwing things, some are (basically anything they can pick up becomes a rock once they ball it up).
... However I find it hard to believe that he can only throw it 5ft away from his reach before he starts to get a penalty. ...
more to the point, i believe the rules are that the range is measured from the end of the creature space, not reach. so something with reach standing in front a line along side a medium creature throwing at targets at the same distance would have the same to hit penalty for range (if using the same weapons).
Ok so my buddy has a large creature and likes to throw rocks. However I find it hard to believe that he can only throw it 5ft away from his reach before he starts to get a penalty. So is there a rule I don't see about the range of thrown weapons for large creatures?
The rules are definitely bias against creatures that are larger than medium and smaller than small.
There's also a ton of feats, traits, and archetypes to optimize thrown weapons, including increasing their range.
Regarding throwing rocks, not sure how you are doing it. There's a Rock Throwing (Ex) in the bestiary, but as mentioned above, it has 120ft of range. Otherwise, it would be an improvised thrown weapon, which means -4 to attack without the Throw Anything feat and has a range increment of 10ft. Improvised thrown rocks are a really crappy option....
Once a long time ago I was trying to come up with a solution to a similar problem here, and I went with something like multiplying out the range based on size.
The rationale being that in this magical world where giants and such live, we don't need to worry about the volume/surface area problem where large creatures can't support their own weight. And then we just consider that the Colossal creature is actually equivalent to a medium creature in a world where everything else has shrunk to fine.
I'm pretty sure my idea was just to multiply the thrown range of the weapon by the ratio of CreatureSize Space/Medium Space. Medium is 5ft, which makes Large x2, Huge x3, etc.
This would make a dagger have a range increment of 60', assuming it was a colossal dagger in the hands of a colossal character. The benefit with basing it off space means that no adjustment is needed for Medium OR small characters, which are the sizes most commonly interacted with.
Alternatively, you could double it at each step, where the thrown weapon would have a range increment of 160'. The nice thing with this approach is that the range increment maintains a constant ratio to the max height for that size listed in the size table(adjusted increment/height=125% for improvised thrown weapons), which is more in line with the rationale behind making an adjustment like this.