Thats what makes it brilliant.
You have to be pretty stupid or immature to read that movie as a Heroic war of the good guys vs the Aliens, and cheer on the Fascist protagonists.
The director is Dutch and remembers Nazi occupation. When he read the book (which is a Fascist bible) he made the movie you saw. He even mirrored shots of Nazi propaganda films in his directing.
It shows how the stupid and unenlightened can so easily fall into fascist propaganda and viewing themselves as the good guys, when they really are not.