There's more to it than that. Semantically, where is a very wide-ranging question-word, covering such meanings as general explanation ('Where will it all end?'), broad location ('Where is Denmark?'), specific location ('Where did I leave my glasses?'), intended destination ('Where are you headed?'), and point of origin ('Where have you been?'). Kids (and some adults) like to play with the ambiguity. Where do you live?' On planet Earth.
Particles help to sharpen the focus of the question. 'Where are you going?' means the same as 'Where are you going to?', but the to emphasises the sense of direction. Adverbs like exactly do the same thing: 'Where exactly...?' The motivation for 'Where are you at?' seems to be a a desire to establish more precisely the location of the addressee. We need to look carefully at contexts to see the motivation. Here's a case in point:
X is on the train, travelling to meet Y, and Y wants to check up on whether he'll be there in time. Y calls his mobile. 'Where are you?' X replies 'I'm on the train'. This isn't specific enough for Y, who can't now ask 'Yes but where are you?' as a follow-up question. He has to rephrase, and one of the ways, evidently, is to say 'Yes, but where are you at?' - where exactly have you reached? Or, of course, to start the conversation by asking the question in that way.
The usage is reinforced by other constructions with a similar end-placed particle, all of which sharpen the focus of the interrogative, such as 'Where are you up to?', 'Where are you from?', 'Where are you near to?', and so on. There may also be some reinforcement from the idiomatic use of the same construction, in which the enquiry is more about a person's state of mind or stage of achievement ('Where are you at?' 'I've nearly finished') or a fashionable event ('Market Street is where it's at'). I suspect most uses of 'Where are you at?' will contain a semantic nuance not present in the simple 'Where are you?' So it's not simply a tautology.