I have occasionally helped transport a person with a wheelchair. I have yet to find a car trunk that will not accept a folding wheelchair. I suppose there are a few, possibly a Mazda Miata or some convertibles or other small sports cars.
Some vehicles, including some hatchbacks will require that the folded wheelchair is stored vertically, not horizontally. This, you might find, makes it easier to place and remove the wheelchair as placing a wheelchair horizontally in a trunk requires fairly substantial upper body strength as well as a good backbone. Check out a Pontiac Vibe, for example. Chrysler PT cruiser and VW Golf are others but the Golf might have a high transom to clear.