Because the thing going on now is that Newgrounds is "everything by everyone". A huge variety of material is here. And yet your ads are all THEMATICALLY the same across the whole website. They're all advertising MMORPGs and online games.
It's no wonder that 600 visits on someone's personal site can make them so much more ad revenue than 1000s of visits on Newgrounds. Take my own page for example - I'm not a very popular flash or music artist, but if I did decide to ramp up my production, the ads on my pages would be completely irrelevant to my art. Even if I did spend time getting people to come to my NG page, why would anyone who was looking to watch a warm Christmas animation click on an ad for a "Free Giant Mecha RPG"?
Under a Project Wonderful system, people could bid on the ad space, and the winning ads would likely actually be relevant to the page (they could be Christmas-themed, for example), which would mean significantly higher revenue.
Moreover, by having a one-theme-fits-all ad system, you are effectively encouraging the thematic homogenization of Newgrounds content. People who make content that does not generate good revenue for online MMORPG ads will be discouraged when they see that their contribution is little-wanted.
Revenue ad-sharing is a great idea, but it could be a lot more effective than it is now.