The rogue officer describing how the Viet Cong were not evil despite committing grossly evil acts can come across as odd. But then again, he was not exactly sane or a good judge of character, and we are not supposed to believe the Viet Cong are good.
The U.S Command sending Willard, a recently divorced and clearly traumatized veteran of the currently ongoing Vietnam War on a top-secret mission to kill a rogue U.S Special Forces Colonel. You would think they would choose another Special Forces guy who didn't have all these psychological issues to take the mission. However, the concept and true impact of post-traumatic stress disorder was only recently coming into the limelight at that point, and before that, most military forces around the world didn't care if you were traumatized by what you experienced; if your body was intact and you could fire a gun, you were good to go. The U.S. military would be no different towards Captain Willard. Even in World War II, PTSD was not recognized and most commanders refused to accept it as it would tamper with their worldview.
Also, in Redux, it's noted that a Capt. Colby is sent to make the initial attempt to stop Kurtz. Colby's background is the complete opposite of Willard's but on arrival Willard meets Colby and finds that the fine upstanding officer and his team have fallen in with Kurtz. It's possible that Willard's already unstable psychology made him safe from corruption.
The part right before the crew enters Cambodia past that bridge can come across as surreal just for the sake of it. But then again, we are looking through the eyes and ears of Private Lance who is currently stoned on drugs, no wonder it was surreal.
While the plot of Apocalypse Now is essentially Conrad's Heart of Darkness, most of the scenes are taken nearly verbatim from a real-life, first person account of the war, Dispatches by Michael Herr. The scene at the bridge is exactly as described, right down to the stoned-out M79 gunner killing the screaming VC with a single, instinctive shot in the dark. The movie was surreal because the war was surreal.
Near the end of the film, while Willard are looking on Kurtz's possessions, he notices the "Golden Bough" book. That one, which says, that you should kill the old priestly king, if you want to succeed him. Supposedly insane Kurtz was perfectly aware of what's happening, his place in this, and that he's gonna die. However, Willard refused to accept reign...
Would one Colonel, no matter how charismatic and skilled, really be enough to disrupt the effort of a war machine as powerful as the American military? The Generals seem to think that Colonel Kurtz is a threat to their operations, but the only thing Kurtz' overt actions are going to reveal is that America has a presence in Laos and Cambodia when they are only supposed to be operating in Vietnam. At worst the Communists will just get a little angrier than they already are, but who gives a shit? They hate you and want you out of their territory already so it isn't like one Colonel is really going to make a difference. Besides what makes the whole affair even more pointless is that the Vietnam War didn't even end in our favor, the death of Colonel Kurtz was entirely irrelevant in the long run!
The movie takes place in 1969, they really didn't know they would draw from the war six year later. They obviously didn't act on facts only viewers know. And saying that the only consequence would be communists getting a bit angrier is really shortsighted. Firstly, it would fuel propaganda in Communist countries (look at what the bad bad America is doing in a neutral country), which would be a blow to the US Cold War efforts. Secondly, it's not just their enemies who would get angry but their allies too (I know the US pretty much wipe their butt with the UN but still). And probably most importantly, the war was already losing support of the US public, this would really not help the army agenda.
Many Veterans have cited this as an accurate portrayal of the Vietnam War.
One of the Air Calvary choppers auto-rotated in near the tree-line shortly before the napalm strike. If the crew survived the crash, they most certainly were caught in the napalm strike.
An elderly Vietnamese couple are watching the medevac'ed Cav Trooper in horror, when the VC Saboteur shoulders past them to throw her boobytrapped non-la into chopper. The elderly couple (who were doing nothing but watching the carnage in shock) are gunned down with the saboteur, even though they had absolutely nothing to do with the deed.
Colonel Kurtz's assassination turns out being for nothing in the long run. The entire reason Willard was contracted to kill Kurtz was so that his methods of fighting in Laos and Cambodia would be kept secret as America wasn't supposed to be there, even though that type of tactic would be beneficial towards achieving victory. America ends up leaving Vietnam, giving up on winning the war, and the presence of MACV-SOG and the CIA's top secret missions going on there end up being revealed after the end of the war anyway. The death of Kurtz covered up nothing. Kurtz had practical military necessity in mind, not his commanders. A model officer and a loving father and husband was killed for no real reason.