Tris had time to grow distrustful of anyone. Blanket suspicion that everyone has their own agenda, because everyone has something that they want, and so her kneejerk response is you think he's telling the truth?- it's plain for Ellie if she looks for it, how Tris starts to say something and then stops. Looks down, biting the inside of her cheek.

"What do you think?"

Ellie's got a feeling of her own in the matter, that much she can tell. On the other hand, after what she's heard and seen of the guy, all Joel wants is to keep Ellie safe, but safe isn't always the right thing to be.