That article seems a touch misleading, as they're stating that anyone who submits their stuff through the "Contribute" site and gets it added to the game will receive profits when the items are put on the store. The fact is that, so far, there are NO standard-submitted community items in the store - the ONLY ones there are the special-case Polycount stuff. Everything else is Valve-made. Therefore, the statement "Anyone who's had their self-made items added to the store has made a buttload of money for it" is true, but not clear on the conditions for getting one's items in the store - so far, you would have had to win the Polycount contest to get them in there.
Personally, I think it's fair (albeit definitely jealousy-inducing :O) that the Polycount winners get this insane amount of money as they won a contest and that happens to be part of the prize package. They made the conscious effort to enter the contest, and upon victory, they were rewarded as the contest hosts saw fit. It's different from simply submitting something for use (which perhaps should also give some sort of monetary reward IMHO, after all it's your hard work they're using; but they do at least give you the "self-made" versions of your things and recognition in the community, so...).
As to why the new models being added with the Art Pass Contest don't get as much (I saw it mentioned): models were never the focus of that contest, and as such Valve sees them as a side thing that happens to just come with the map (sad, perhaps, but true). If they pay less to the winning Art Pass mappers, it's because, while the Polycount people's items earned cold hard cash for Valve being sold through the Mann Co. Store, maps are added and distributed for free, thereby making no money for the company, thereby not providing anything to split with the creator(s).
TL;DR - The article forgets to mention that the only community items thus far added to the store have been the contest winners, NOT standard-submitted stuff. The Art Pass Contest wasn't about models, and as unpleasant as it may be to realize it, Valve probably sees any models added as a result of new maps being added as a relatively minor side-addition.