Is Apocalypse Now, an anti-War film or a pro-War film?

This is going to be subjective at best, because (as you've pointed out) any movie can be interpreted any number of ways in order to facilitate a certain goal.

Fahrenheit 9-11 features an interview with a serving US Soldier who states that, in homage to the film, their tank division plays loud music at the enemy as a way of intimidating them. The song he claims most effective is Drowning Pool's The Roof is on Fire: but it's impossible to prove from this that Drowning Pool in any way intended for their music to be 'pro-war', its all about context and how the text is dispensed. The song used in this video is the Bloodhound Gang Cover...

It's true that the 'Charlie don't surf' sequence is frequently cited as a emotionally-inciting sequence by service personnel, largely due to its depiction of unopposed, effective military aggression:

Depending on whether you'd rather hear the intention of the movie, director Francis Ford Coppola is fairly certain he has made a politically neutral film in this respect:

"I feel any artist making a film about war by necessity will make an 'anti-war' film and all war films are usually that. My film is more of an 'anti-lie' film, in that the fact that a culture can lie about what's really going on in warfare - that people are being brutalised, tortured, maimed and killed - and somehow present this as moral is what horrifies me, and perpetuates the possibility of war."

Whilst Coppola won't go as far as to claim he has made an anti-war film, his sentiment towards 'the horror' of war (both within the narrative and in the quote above) suggest that, as an artist, his disposition is inherently against war. Whether we feel that this is being communicated through the text, and if it is how successful or persuasive we find it, is a matter of personal opinion.

Apocalypse Now is based on Heart of Darkness, a Victorian novel which focused on the corrupting/debasing power of colonialism not only on the colonized (which is obvious, at least to the colonized) but moreover on the colonizer (somewhat less obvious to many, at the time).

Certainly colonizers, then as now, rarely give up their colonies willingly. because they get stuff cheap. It's like stealing, only worse.

Upon this theme, Apocalypse Now lays on the Vietnam War, an external imposition of cultural and political hegemony that can serve as colonialism's younger brother, with the same sort of attendant evils.

Lording it over people tends to make the overlord rotten. Did the US, as every other nation before it.

And so, heck yes, it's anti-war. :)

The only clear message in Apocalypse now is that war is hell.

Different people will take that as pro or anti war.

A soldier might see the depiction as positive as the difficulty of fighting makes war more glorious: it wouldn't be heroic if it wasn't hard.

But an opponent of, for example, the Vietnam war might take the opposite lesson: war is brutal and messy and we have no business participating in it given that the mess we will create and the damage we will do is disproportionate to any gains we might win.

This is entirely consistent with Copplola's quote that it is an anti-lie film. No war, especially Vietnam, is without cost but governments often make war sound like a glorious cakewalk with few costs. Apocalypse now undermines any such propaganda.