I have been transporting my bike in the rear of a Ford Transit Connect for the past 5 years with the front wheel off and there is no damage to the bike or the wheel. The best way to transport the bike is to place a piece of plywood or presswood on the floor and put a bike mount on it. You may have to fold down one of the seats to get the bike in.
Here's an old photo of my Ace in the back of my van. My bikes stay in the van all the time so you probably won't want to put a full plywood floor as I did.