In any case, her taxes would go to the Exchequer, just like Tony Blair's do. The Queen can't just walk over to the Treasury and grab a pocketful of tenners whenever she feels the urge to go and grab a pint.
She is also paid a stipend by the exchequer. Yet in some sense as Queen she "owns" the government. I'm not exactly sure how to word it but this is as close as I can get. I suppose it is part of the evolution of the monarchy from totalitarian rulers to national treasure.