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.