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.