The story revolves around the concept of a fake reality-- a computer system called The Matrix-- that most of humanity unknowingly lives in. Physically, they're floating in human warehouses, but according to their perception, they are operating in a world very similar to ours.
The reason The Matrix is so intriguing--and disturbing-- is that it implants a fear in the viewer that he may be under a similar illusion. How do you know you're really seeing this screen with your own eyeballs and not actually floating with a bunch of wires somewhere in a pool of goo? The film had a lot of fun with the premise without being completely devoid of plot. And even though it never really settles on a particular worldview or message, the movie plays with some interesting worldviews and ideas.
If I were grading The Matrix for cohesiveness and quality, I might end up giving it a 7 out of 10. But as a viewer who really enjoyed this and was willing to overlook the flaws I mentioned, I'm giving it an 8 out of 10.
With a good enough premise-- and execution of the premise-- even otherwise bad movies can deliver.