Basically, like Eliot's Tradition and the Individual Talent and much of the criticism that followed, Freddy got Fingered posits the creation of innovative art and literature as an process of rising up against the prior generation and overthrowing it. But, armed with 100 years of psychoanalysis and nearly as many of surrealism, Tom Green goes a step further and suggests that art-making is part of a near-Oedipal struggle. Tom Green integrates this message into a traditional gross-out comedy coming-of-age story, except everything is taken to its extremes: Tom Green is too old, the surreal elements of animal sexuality, bodily function, etc. are presented with nearly no form of censorship or double-entendre, etc.
Basically, Tom Green achieves two goals in Freddy got Fingered: to posit the creation of art as a way to overcome repression within the family, and to literally make art (the film itself) that doesn't reside in the terrain of horror and comedy and show the edge of the repressed subconscious, but rather puts the socially unacceptable right out in the open. So the film's story is a tremendously optimistic one of art's redemptive power, while the film itself is a disturbing assault on the audience that troubles this notion of art setting things right. Since the film is semi-autobiographical, Tom Green is at once promoting himself and his talents while suggesting that he's a lunatic that the audience/society should hate. I believe he meant this with a measure of self-deprecation but critics read the film otherwise.
If anyone's interested, I can develop this argument, but the Oedipal side of it basically boils down to the basic father/son story conflict, Gord's weird attraction to animal penises, Gord's destruction of his family from the inside, the "cheese factory" job where, at his parents behest, Gord is surrounded by old, sexless women while he waves around a massive sausage, and the "Daddy would you like some sausage?" scene where he asserts the power of art by creating something that is at once disruptively creative and full of overt sexual imagery. Notably, it is at this moment when he creates art that society (Dave Davidson) values. This all resolves itself in the elephant scene, obviously, where Gord's wild fantasy ends with him attacking his father with a massive animal penis before the two can return to society. The sandwich motif throughout the film is related to this, too.
The other side of the argument (that the film parodies gross out comedies and questions their value by taking their conventions to their logical conclusion) is basically proved by the fact that the movie is really gross, really on-the-nose, and not always straight-forward funny.