You should use "I hope not."

I agree with JK. The real problem is that the sentence "you won't miss the train" contains a double negative: "will not" and "miss" are both negative ideas. There is nothing wrong with this but it makes it difficult to formulate a sensible reply. Any reply to a sentence containing a double negative is susceptible to misinterpretation. The best way to reply to such a sentence is to present a complete thought: "I hope I don't miss it"

"I hope so" makes it sound like you might want to miss the train. If that's not what you want to say, you should use "I hope not" or "I hope I don't."

What are you talking about?I don't understand.