I think a lot of problems critics have about the list is that they're confusing popularity with influence. If this was a popularity contest, then Trey and Matt, Seth, Matt, Mike, and others would definitely be up there.
They made a truckload of money and pissed a lot of people off in the process, both in the content of their wares and those within the animation community. They're powerful, but does power begot influence?
Depends on how they wield their power.
Trey, Matt, and Seth entertain folks, but I don't think they're really influencing folks or changing the industry as a whole. They're making deals, yes, but influence? No. I mean, if you want to get into it, I think Aubrey Ankrum, Rhode Montijo, Kenn Navarro, and the Brothers Chaps are way more influential than Trey and Matt and Seth in one segment of the creative community. And if you know those names, then you know what I'm talking about. If you don't know those names, then some time in this decade, you have encountered their works (Ankrum, Montijo, and Navarro were the creators of Happy Tree Friends and the Brothers Chaps created Homestar Runner).
I love this list not just because I'm part of the rabroad crew, but because it's not filled with the usual suspects and is a very eclectic group of individuals that are rarely acknowledged in the media and by this community. I mean, personally speaking, I'm a fan of Fred Seibert, who helped mold the modern television animation landscape more than anyone realizes. But how many people knew who he was without resorting to Wikipedia for research and beyond Frederator?
It's not a popularity listing, it's a measure of influence, those that made an impact beyond personal gain or social commentary in the animation industry as a whole.