Danny Boyle's film probably has the most blatant "message" in it, due mostly to screenwriter Alex Garland, whose novel The Beach (which Boyle also directed as a film) wasn't exactly subtle in its depiction of paradise-gone-wrong. 28 Days Later starts off as a rather focused and personal story of a small group of survivors who have instinctively become a surrogate family, learning that the most important thing in surviving such a nightmare is to have each other. Who would've thought that Boyle needed to end the world to show that he was such a softie?
The film's third act, however, takes an even more sinister turn, introducing an evil and horror more powerful than those infected with the rage virus. Yes, the evil lies within us, the supposedly intelligent and humanistic un-infected, as illustrated by Christopher Eccleston's rogue military outfit. Visions of the New World, in which the army boys are now the Super-Humans, plague what could be a relatively safe and comfortable living environment for the civilian survivors. This God complex leads to insanity, and, of course, forces our hero Jim to take matters into his own hands to such violent extremes that we eventually can't tell him apart from the infected.
This is actually the most disappointing aspect of the film, and the whole section feels a bit rushed, as if Boyle and Garland realized they only had about a half-hour left to actually have some sort of "message" for their film. The resulting Lord of the Flies angle is an easy way out, certainly, but perhaps an unavoidable aspect of such a film. It was inevitable that the humans would be portrayed as the true horror - isn't that often the point of most horror films?
And thus concludes Zombie Philosophy 101. The most important thing to keep in mind with all these ideas is that they are in no way essential to your understanding and enjoyment of the films. They are fun, entertaining, exciting horror films first and foremost. We've pointed out the thematic elements only as something to keep in mind as you watch the movies and perhaps form your own theories of what the filmmakers were possibly trying to convey. They're "smart" films, yes, but not too smart to forget to have some fun.