The Matrix changed just about everything when it was released in 1999.
Let's start with the obvious. That summer was supposed to belong to Star Wars. The fact that The Matrix happened probably goes a long way to explaining why it was so easy for Star Wars backlash to happen, the first of several blockbuster movies to steal the thunder from the original escapist blockbuster.
But rather than dig into that thorny debate, let's just have a look for the moment at The Matrix itself. At the time, everyone was impressed by three things about that movie: 1) Keanu Reeves was actually cool again, 2) philosophy in an action movie, 3) the action.
The first point explains itself, and Reeves has settled back into a nice little near-anonymous groove, reliable in a Hollywood-several-strata-down kind of way. The second point is the reason the sequels could never have captured the same level of approval as the first one, because everyone assumed that all they really needed to know or care about was the idea of claiming destiny in the face of a massive existential crisis, a crisis the audience was invited to share. The moment the sequels took everything and moved it forward to an actual conclusion, the Matrix became an intellectual quagmire to anyone who just wanted their big ideas delivered with minimal investment. (Lesson learned: in pop culture, keep your thoughts to a superficial level.)
The third point, oddly, gains considerable steam in the sequels, especially the final one, when everyone flat-out said that final Nero-Smith fight was the Superman brawl that never happened. It famously didn't happen three years later in Superman Returns, either. It was the fulfillment of the promise from twenty years earlier, when Superman battled General Zod. In short, The Matrix helped make the modern superhero film genre possible.
Previously I've gone into detail about the evolution of the genre in film. The short of it is this: by 1999 you did not believe that a superhero could be taken seriously.
Almost directly after The Matrix, Bryan Singer's first X-Men effort was released. It was a spectacular example of first steps. Three years after The Matrix, Sam Raimi's first Spider-Man effort was released. Here's where the Wachowski effect was really felt for the first time (other than in Crouching Tiger, Hidden Dragon, but that's a story for a different time). After the near disaster of Spawn, this was the first time superheroes benefited to a considerable extent from CGI animation, so that their reality might actually feel realistic to audiences. Audiences came out in droves. Batman, who had helped usher the second wave of superhero films and had helped sink it, wouldn't be seen again for a few years. This was no longer his world.
Marvel's brand of superheroes started to take over. Marvel is known in comic book circles as the House of Ideas. It famously ushered the "Marvel Age" of comics in the 1960s, and didn't even let bankruptcy slow it down, still enjoying a considerable amount of success with the same basic formula today, infusing sensational characters with classic monster movie origins and a healthy dose of human pathos in essentially stereotypical superhero adventures. This is what it brought to movies at the start of the third wave of the film genre.
Yet it wouldn't have been possible without a movie that isn't really a superhero movie, but might as well be. Audiences might have themselves been confused, especially when Neo flies off at the end of The Matrix, which might be interpreted as a superhero origin story all its own, separated from those pesky sequels that leave him in that same world with the same problems, rather than letting him zip around, using his awesome new powers in more conventional stories. Superheroes, especially Marvel superheroes, always start out like that, before going into patently conventional stories. They never stick around with the shock of the new that inform their origins. (Ah, and never mind that Neo has the most conventional superhero stereotype of them all, a recurring foe in the form of Agent Smith, fighting him in some climactic fashion each film, because there's something to be achieved, rather to simply be done, each time.)
I'm not saying any movie derived from a Marvel creation is completely worthless (although The Avengers is absolutely the culmination of what suddenly became possible because of The Matrix, without being much more than that). You can believe that superheroes can look realistic now. That's how Batman ultimately came back, because he took that realism to a completely new level, thanks to Christopher Nolan. Perhaps it's telling that superheroes have become the new action heroes, as they were when they first appeared in comics, and not just costumed characters who come from a source most people don't respect. The Matrix may have been the last great action movie, and like the films it inspired, it was more than that, but most fans didn't like to be reminded.
Well, maybe you're convinced by this, and maybe next time I'll have to make another, perhaps equally tenuous argument about Agent Smith being the next logical step from Quentin Tarantino (and maybe now I've got someone saying, "I want to read that!"), and maybe I've got you wondering what you missed in those other Matrix films. Sometimes expectation is its own reaction.