Yes, Ned can hear the affection in that name-calling. It's not the sort of thing he could really get away with, with Daneel - he's far too literal-minded to understand that sort of thing - but he recognizes it for what it is. What Charlie says about Meyer being a control freak just confirms what Ned has observed in him thus far, and Charlie ought to know.

Interesting, how quickly Charlie progresses from Meyer's need for control, back to the situation the three of them find themselves in (in which Meyer's control is limited), and on to his not-so-veiled threat. Of course, Charlie is a product of the same culture that Meyer is; he must think there is danger to himself, to both of them. But to Ned, it seems that the main impulse behind the threat is fear for Meyer, wanting to protect him, to guard him.

He would find it touching, really, if it weren't for that sudden spark of terror deep in his chest when Charlie looks at him like that. Ned's not afraid of Charlie anymore: not regularly, anyway. Hard to maintain that kind of attitude when he's seen Charlie falling asleep like an overtired toddler, when he's seen him drunk and convivial, when he's seen him a scrawny teenager, in Meyer's mind. All the same, there is a shard of the fear in Ned - bright and sharp-edged - that remains a few inches underneath the surface, easily unburied.

So Ned pales at Charlie's threat, nonspecific though it might be, swallows because his mouth has suddenly gone dry. "Right," he echoes.