Ebert's point is valid and I'd say he'd be right if he were to say a truly artistic game hasn't really been made yet. There's certainly been artistic endeavors in videogames, with mixed success. I mean, when he says, "I am prepared to believe that video games can be elegant, subtle, sophisticated, challenging and visually wonderful," does that sound like an insult? It's not, he's just saying that games don't quite reach the caliber of art. Keep in mind, also, that things that have very crude or simplistic craftmanship can be considered art as well.
I'm also very wary about citing Tim Schafer's games as "art". His style relies on a very tried-and-true narrative style and doesn't really ever directly tackle the problem of player interaction very elegently. Instead his games are content to sideline the player into a slightly more observational role in order to get the content of his stories across, which, of course, makes for an interesting story but the game itself becomes of arguable quality.
Ebert is right in that the player-interaction is a big hurdle, but it's not necissarily an impossible one. I seem to recall film had a similar problem, in using pictures of reality to craft a story that is complimentary to the medium and could be considered "art". Film may not seem like a weird idea nowadays, but back when it first strated it certainly was. I'd postulate that games are in a very similar position at the moment, where creators are just beginning to realize and tackle the problems in realizing games as an artistic medium (and I'm not talking about bootstrapping cinematics into games, which many developers seem to think is acceptable at the moment).
It's no big deal to see critics of other mediums react this way, though. All mediums have this problem and get labelled as gimmicky trash (and, sadly, some either sputter or flat out don't overcome it, like comic books and animation in America). It's a little disheartening, and current gamers will probably never really get the satisfaction of seeing the critics eat their words (becase they'll probably be dead by then), but games as an artform will happen.