It’s actually hard to take it at face value. After working on the Teiva for 120 years while facing criticism and being the target of many jokes, it’s really hard to think that he too doubted it.
My way of understanding it is that he thought it will work out in the end. He figured Hashem won’t pull through with the threat and He’ll scare them or work something out. This is similar to the way children often think of their parents’ wild threats. It’s not that they question their parents’ ability to turn around mid-trip. They just don’t envision it actually happening.