He's more than willing to give Sugata the benefit of the doubt that he knows what he's doing, so there's no protest from Shinji, not that he'd be able to voice one very well in his current state.

He finally felt his breathing calm down a little bit once his lungs were clear, or at least mostly clear, of water, and he draws a few long, shaky breaths to try and steady his nerves a little bit. It... doesn't really help a whole lot, but he does manage to utter a small, "Th-.... thanks."