Many fantasy novels deal in pure fantasy, meaning that they invent entire worlds. In the typical fantasy novel, the world inhabited by the characters may resemble our own, but it will generally be a completely different world, especially when "fun" or interesting objects such as transportation are concerned.
Harry Potter conforms to this when it comes to elements like dragons, evil warlocks, etc. However, a main theme in the Harry Potter series is that of common objects made magical, such as a magic train accessible through a secret entrance. The flying car fits into this nicely but goes against the usual expectations of fantasy.
There is an unspoken general theme amongst fantasy works which dictates that great fantasy works don't take place in a modern society which is relatible to the modern audience. This is because of the author attempting to take the audience away from reality and into the world that he/she has created. This is the reason that authors use parallel universes or different time periods that we cannot directly relate to. By using a car which is so common and relatible to our own society in the magical world it is linking reality to fiction and also taking our reality and altering it as opposed to simply taking us away from it. It is for that reason that the flying car goes against our expectations, not to say that this is unheard of in the fantasy genre but it is a powerful and surprising tool.