Well, the dialogue really is completely ambiguous on the issue. Jim just trusts that his son knows exactly what can and cannot be done - so if he shoots down "beam over and stop", there's no point in asking for specifics. David knows that something about it is impossible, and it might just as well be the beaming part.
Of course, David is by training a Genesis specialist, not a Mutara nebula specialist, so any inability to use the transporter would probably be Genesis-derived rather than nebula-derived. Then again, David has apparently lived for quite a while as next-door neighbors to this nebula, so we can't really tell what he knows about it...
Writer intent is pretty obvious here, even though the dialogue is not - but that's no reason to stop looking for clever excuses for why the movie wasn't wrapped up a few minutes sooner, with a bit less anxiety.