It was made clear in the movie that they were paramilitary (hired protection), and not an arm of the US.
They were there because the animals were very dangerous.
The Na’avi were also defending their homeland, but trying to cooperate with the representatives of the corporation. The confrontation was when the corporation decided to blow up the Na’avi’s only home.
As you say, it’s just a story. There are many, just like it. The big attraction was the visuals.
what animals? Weird scary creatures chased our hero around until that blue girl saved him ... but we never saw them again until the mean military/capitalist junta started a war and for some reason they re-appeared to fight for Pandora???
I recommend it for visual beauty and effects, but the stupid stuff was too much to count.