The meanings are different. 1. You are taking her with you, aren't you?" It means, "I expect you to"; "I want you to". 2. You are taking her with you, are you? Two possible meanings: a. You are just repeating what the other person has told you, just to make polite conversation. Example: "My husband is a lawyer." " Your husband is a lawyer, is he?" This technique is used by politicians and royalty when they meet people at a garden party or on a walkabout. b. It means, "Oh, is that what you are going to do? I didn't know that."

You're right about the general rule. In this case, I couldn't say for sure without knowing the context, but it seems to me like the speaker may be challenging the other person -- suggesting that taking her (is it a person or a vehicle / piece of technology?) would be a bad idea....