You're right, a single line or reference in a movie can stick in the craw despite what the rest of the film intends.
The President's speech in Independence Day came over to many as jingoistic, despite the fact that the whole speech was reiterating that the whole of humanity had to band together to deal with the threat, and America couldn't stand on it's own. "It will no longer just be an American holiday."
Sometimes people miss things like the fact that British, Israeli and Iraqi pilots were together on one base in the desert, at a time when Iraq was still a Big Bad Evil Nation!
Saving Private Ryan got criticized because they did not show the British on D-Day, yet it was an American Operation, in the American Sector of the campaign. Be a little like complaining The Dam Busters didn't have B17s!
Now, Objective Burma and U571 on the other hand...