The movie's focus is on a Mutant Registration Act being pushed through Congress. There are staunch supporters on both sides of the argument, and like every good argument, there are even radicals. With such an large cast, it is really hard to pin down who the main character is, as with the comics providing a ton of back story for every individual character, some things had to change or be left out completely for the film to make a transition from page to screen.
First off is Rogue. In the comic books Rogue was actually an enemy of the X-Men to begin with, but ended up defecting towards their 'side' later on in her life, around the age of 27. In the film, Rogue is a mere teenager who is just trying to find her place in the world, eventually stumbling across the path of Wolverine during a hitchhiking trip to Alaska. It is also revealed in the comics that Mystique, a villain in the film, was actually Rogue's foster mother at one point.
Another character with warped continuity from the comics to film translation is Storm, or Ororo Munroe. In the comics, Storm is a big player in the overall universe continuity, as she is married to the Black Panther, making her the Queen of a fictional country called Wakanda. But that is long far into her story. She actually started off as a revered priestess of a small African tribe in Kenya. While she was apart of the 'original' X-men, the movie seems to ignore all other parts of her story, although she does get some rudimentary character development in the sequels.
These changes in continuity don't mean that the film itself is unwatchable. It is actually extremely entertaining, with classic fight sequences and fantastic special effects. One scene that stands out in my mind is the opening scene with Magneto discovering his powers. Magneto is Jewish, and happened to be a victim of the holocaust in World War 2. The opening scene is where he discovers his powers, bending and breaking the metal of a gate. It is a very powerful opening, and really sets the tone for Magneto and gives his character fantastic depth for what he believes is going to happen with mutants once the world figures out the ethical implications of having such powerful individuals present.