In short, I don''t think the Matrix was a fad. Now here''s my reasoning.
If you consider a fad to be something that is widely popular for a brief period of time, and then fades from memory, I don''t think that will happen with the Matrix.
The closest historical reference I can think of is Star Wars. It originally consisted of 3 movies, released over the course of a few years. It was a huge pop-culture phenomenon to the extent that you could make a Star Wars reference 10 years after the 3rd movie, and everyone would get it. I think this will be the case with the Matrix as well. Star Wars remained a part of pop-culture for nearly 20 years before another movie was released, and continues to be.
As craeonics mentioned, there are endless references to "Matrix style" visual effects. Whether you believe they are founded or not, this is a case where perception is reality. Slow motion wire kung-fu, and "bullet-time", will be forever tied to the Matrix.
Now here is where Star Wars and the Matrix differ. Star Wars was targeted at general audiences, with its PG rating. The franchise was heavily supported by the wide range of toys that many of us probably played with as kids. At that time, everything from pillow cases to underwear had images of Darth Vader or Yoda on them. I clearly remember playing out Star Wars scenes with my friends at recess in the second grade.
The Matrix, on the other hand, was aimed at older audiences. From its deeply philosophical story, to the graphic violence, it''s just not a movie you can show, in its entirety, to a 6 year old. The toy offering I''ve seen appears to be designed for collectors in their 20''s or older. They seem more like display pieces than toys a kid would play with.
Unlike the relationship I''ve had with Star Wars since Kindergarten, I don''t the Matrix will be such a big part of the younger generation''s childhood.
That aside, I still believe that the Matrix has made a big enough impact on pop-culture and modern action film making, that it will not be forgotten for many, many years to come.