No, not inherently. It just means you accept the other person's reasoning and won't talk about it anymore. It could be rude or annoyed depending on context or tone of voice. It can mean that you don't agree with the other person but feel discussing it further is a waste of time.

Depends on usage. Lots of ways to use in a way that isn't rude. "Why would you take the bus?" "My car is in the shop and it's right on the route. " "Ah, okay, fair enough. "