For cars that store their spare tire in a well inside the trunk, that seems like a good place to put my tefilin while driving -- it takes up no extra space (if they fit in the middle of the tire), keeps them from rolling around, keeps them covered (of course you risk forgetting them there!).
Assuming they're not getting dirty or greasy -- any reason (practical or halachic) not to do so? Yes they might end up smelling rubbery ...
