You say 'Tom won't be late, will he?' when you are assuming, and hoping, that Tom won't be late. Two possible replies are 'No, he won't' or 'Yes, he will'. You say 'Tom will be late, won't he?' when you are expecting Tom to be late. Perhaps you have received a message telling you that he'll be late, and you are confirming that this is true. The replies are the same : 'No, he won't' or 'Yes, he will'. The 'No' or the 'Yes' in the reply relate to the grammar of the sentence - 'no' for a negative sentence and 'yes' for a positive sentence. They do not refer to whether the speaker is correct in their assumption or not. They don't mean 'Yes, that's true' or 'No, you're wrong'. They simply echo the grammar of the sentence.

Basically, at the end of the sentence, you ask if the opposite is true. It's a way to ask for confirmation. Example: Today is Monday, isn't it? ==> Yes it is. / No it isn't. Today isn't Monday, is it? ==> Yes it is. / No it isn't. In your example, it's exactly the same rule (won't = will not).

SuKi is right as usual, isn't she? I definitely do not mean this as a question. It's a statement. SuKi is right. "Tom will be late, won't he?" is probably not a question either. I probably know Tom well, and know he is often late! If I am not absolutely certain he will be late I can put a little more 'question' intonation into the sentence. I'm sort of checking if he's going to be late - but I still think he probably will be late. So, to me, depending on how it's said, it ranges from a little bit of a question to a definite statement of exasperation! I may not even expect a reply. "Tom won't be late, will he? is much more of a real question. I'm checking if he will be late. I'm probably worried he will be late. I'm probably really asking someone for information, or for reassurance. I would expect them to reply to me in some way. You need to know the situation/context to know which one works best.