I'm not brought to tears of fitful rage by Ebert's comments, but his objections all boil down to him simply not understanding the medium he's critiquing. The real problem is he's attempting to rationalize his dislike, and that turns it from "I just don't like 'em" to "Games will never be anything more than a distraction and here's why." Or, to put it more plainly, he's framing opinion as empirical truth, and that's what upsets a lot of people.
Had he simply emphasized that to HIM games would never be art, that would've been fine. Crotchety old man cannot immerse himself in a concept that was in it's infancy or even nonexistant most of his life. But he attempts to justify his position, and thus opens himself up for debate. On the field of debate, he brings three small games, one of which I'd never even heard of, and offers them up as the ambassadors of their medium. I could just as easily say that cinema has not become an art form because of Glitter, All About Steve, and Boat Trip.
There are concepts that simply can't properly exist outside of video games, as video game-based movies are so quick to remind us. Games like Silent Hill 2 and Ico need the medium they exist in if they are to become fully realized as art, just as a movie could not convey the Mona Lisa and a comic could not adequately convey The Nutcracker(though I'm sure a comic by that name probably exists).
Now, do games like Silent Hill 2 and Ico represent the pinnacle of gaming artistry? Doubtful. They are some of the best things we have now, and I would consider them equivalent to many great literary and cinematic works, as they do what many of those fail to: elicit emotions from their audience. Silent Hill 2 is genuinely frightening and atmospheric, and Ico manages to juxtapose the grandiosity of a large, complex castle full of shadowy opponents and a struggle for survival with the sweetness of a young love story of sorts. But they stand at the beginning of a very long journey, and much will change between now and fifty years down the road. Maybe they'll be considered the equivalent of The Epic of Gilgamesh one day, but recognition of truly great artists is normally rewarded retroactively. King Kong was the cat's ass back when it was made, sure, but it wasn't until much later that it was recognized for how monumental it was. Same with Citizen Kane, or Ulysses, or Starry Night. No matter the art form, it is generally appreciated in it's time, but it is only with time that we can decide whether or not something truly stands out as great.
Ultimately, Ebert doesn't appreciate video games for the same reason I don't appreciate Broadway musicals: they don't speak to either of us, and we find ourselves unimmersed in them. But then, I also don't go around telling ballet enthusiasts what they enjoy is definitively "not art."
Still, as an opinion, and not a declaration, what Ebert says is not without merit. It should just be seen as what it is: a movie critic who doesn't see games as art. Or, alternat title: "Grumpy old man is old and grumpy"