Magical trains are more acceptable -- less incongruous, so less of a joke on their own. And are starting to acquire the patina of nostalgiac Romance as they move into the past for a lot of us, which also helps with the magic touch.
But then, they are also different in many other respects. A magical thing must be metaphorically appropriate. Now, a train is a form of transport, but unlike a car, it's a form of transport to a fixed, definite, and predefined point. Most characters would be cast as passengers, have no role in controlling. So a trip to the North Pole works metaphorically best on a train. Still more a trip to Death. You can approximate it with a bus, probably (hmm -- Harry Potter had a magical car as an oddity, but a magical bus was routine business), but for a car, you would need a limo, which would have baggage of its own.
A car is much more free form and under control. Hmm. Like a flying carpet, or a winged horse, or a magical broomstick, or a hippogriff. Another reason why there may be fewer magical cars is that its metaphorical nature already has been expressed in magical form, many, many, many times. But there's nothing else quite so clear that your character will be -- ehem -- railroaded on the path. Even on a boat, you can sometimes prevail against the current and wind.