In this day and age there are various issues confronting people. Some of them involve political opinion. Movies often attempt to influence public opinion on political issues by winning an audience over to a character and then her beliefs. Then they make the symbol of the opposing side into a "bad guy". Sometimes, situations in movies are used as metaphors for certain modern political good guys or villains. In this environment it is no surprise that there are different and conflicting "messages" portrayed by the movies. If you saw certain movies back-to-back and thought about what the metaphors stood for you might feel a little uncomfortable at your own inner conflicts.
Avatar is about a planet of indigenous creatures called the Navi. In this world, humans are alien and are trying to exploit the resources of the planet Pandora. In the process of exploitation there happens to be a very large tree home in the way. The humans are determined to remove the tree and obtain the precious "unobtanium" beneath it. This is destroying the most important home and symbol of their culture.
This movie portrays the invaders as ruthless inconsiderate bad guys and the indigenous people look pure, innocent, wise, and somewhat pacifist. The messages here seem to be about certain countries using their military might to bully less powerful ones. We call it Imperialism and it has been a factor throughout the history of the Western World. But the parallel doesn't end there. It seems likely that some might be thinking "what business does the US Military have in overseas occupations like Iraq and Afghanistan?"
On the other hand, Star Trek seems to have a lot more sympathy for civilization. Captain Kirk seems to find himself either fighting to save civilization from destruction or asking aliens (who are worthy enough) to join the coolest thing ever, the "United Federation of Planets". The mission of "Star Fleet" has an imperialist sound to it:
"To explore strange new worlds. To seek out new life and new civilizations. To boldly go where no man has gone before."
Seeking out new life seems to mean 'to get them to join the UFP or vaporize them'. In fact, the races that refused to join were either savage (Klingons and Romulans) or don't have real bodies (the Organians and the Q).

Pearl Harbor has a very different message than Avatar. That is, pacifism can get you killed. Those brave home boys are out there protecting the country from the savage Japs who don't even have the decency to send a letter before bombing your stuff. The message includes the rally that we have to be willing to fight to protect our "way of life."