Wolverine has said he's "afraid" of swimming because he's vulnerable in the water and can drown, but why is he afraid of flying? Is it an unexplained phobia or is it explained in any comic? We all know why Indy's afraid of snakes.
There's no mention of this fear of flying in the comics, the film scripts, the film's novelisations or the various graphic novelisations. As far as Wolverine's evident fear of flying is concerned, it seems that that was purely an invention of the actor Hugh Jackman.
The 45-year-old Hollywood star admits he even incorporated a fear into his X-Men character Wolverine because he didn’t want to play someone who isn’t capable of feeling scared.
“I put a fear of flying into Wolverine that wasn’t in the script. I thought, ‘I can’t like somebody who isn’t scared of anything.’”
Wolverine is afraid of flying. Are you?
No, I love it. I never get scared. But I came up with the idea that it would be kind of interesting if Wolverine hated flying because it’s unnatural for an animal to fly.
Interestingly Wolverine director James Mangold specifically spoke to your suggestion that Wolverine's fear of flying could be related to his known (and canonical) fear of water but he seemed unaware that the fear of flying was actually Jackman's invention!
What about - Logan on the plane - he's so nervous. It occured to me when I was watching this the first time that if he falls into the ocean that he will drown and come back drown and come back - is that why he doesn't want to get on planes?
I don't know. They told me--everyone who's really knowledgeable about Wolverine has always told me--he hates flying. And Hugh was like "I hate flying"--I mean, as Wolverine. I love the idiosyncrasy of it - that's the beauty of him, I think, the beauty of Wolverine. It does separate him from the kind of Batman, indestructible because of my gizmos or Superman indestructible because I'm indestructible.
There were several references in the comic book series, he never specifically said why other than that flying was unnatural. As for water, he was in the water a lot in the original comic series. The movies have several flaws when compared with the original comic series.