I'd suggest remedying this with one of the following:

1) A blunt, in-your-face text message or demo animation to tell the player it's definitely going to burn vines
2) A Half-Life 2 style introductory puzzle or sequence where vines get burnt in a manner that clearly demonstrates this to the player without actually explicitly saying "You, do this"

I appreciate that walking up to the vines near the start does mention that you'll need something to burn them with, but that was quite a while ago. The comments for the script to suggest making it an objective, so that'd be a third option, if we're going to have an objectives system.

Yeah we came across this problem earlier. There is also the issue of the player running out of flamethrower fuel before they reach that part, halting the player's progress. There was some discussion here: viewtopic.php?f=41&t=2312&start=100

Personally I would go for the Half Life 2 demonstration option. Clogging the underwater tunnel just after the flame-labs with vines should be fairly obvious.

There are flame bursts (Well, since I last played the wad) when you approach. Maybe have one of said burst burn some vines?

Burning some vines out of your way to access the flamethrower would be a good HL2-ish implementation, IMO.

Dunno how proper of a fix it is, but the exit to the flame area is now blocked by vines as well so you have to use it to get out. There's also a fuel dispenser you can use if you get < 50 ammo, so you can't get stuck.