If they wait a while, the boy may become calm and more comfortable. (not just yet though.) At that time, he may be able to fly. At this time he is nervous as a person in a plane. That would be made worse if he flew it.
Not just yet = not now but maybe later
Just is added to other things dealing with time
Just now = only a moment ago, seconds ago
If you look at it in some other phrases, you will see a pattern...
Just kidding = kidding, do not take this as a beg deal
just a minute = not long from now
just decide = do not make a big deal out of it, pick something
just a dollar = it is not much money
You can see that all the time it is used, just means "a little' or 'not much of an issue."