Qui-Gon loosely wraps an arm around Ezra's shoulders in return, careful to give the boy room to move as he pleases.

"Would you like to try speaking to me about what is worrying you, first? Perhaps I can help."

Whatever is plaguing Ezra was enough to make him seek company in the middle of the night. If he didn't want to talk about it, that's fine enough, Qui-Gon won't force him, but if he could provide some sort of assistance... all the better, no?