According to Chris Suellentrop of Slate, it's this:

The real source of the fascination with The Matrix is that, despite all appearances, the movie is not a dystopia. Rather, it's a utopia, a geek paradise. The Matrix is a sci-fi John Hughes movie, in which a misfit learns that he's actually cool. (Think Harry Potter with guns.) At the software company where Keanu Reeves works, his boss might as well be the principal castigating Judd Nelson in The Breakfast Club when he says: "You have a problem with authority, Mr. Anderson. You believe that you are special. That somehow the rules do not apply to you. Obviously, you are mistaken." Of course, we learn that the oppressive Figure of Authority is the one who is mistaken. But instead of going to the prom, Keanu gets to pack heat, learn kung fu, wear a black trench coat and sunglasses, and, to top it off, he gets a hot, ass-kicking girlfriend who sports fetish wear. What kind of dystopia is this? No one wants to be Winston Smith in 1984, but everyone wants to be Neo (or Trinity, or Morpheus) in The Matrix.

Nothing like a little geek psychoanalysis (are we really that hard to figure out?).

Anyway, it's still a pretty interesting article, with lots of good links. Have a look.