It is often a tight fit to put two bikes (less wheels) in the trunk of a mid-size car. One would need foam to separate the two. Putting bikes inside a vehicle where one might be able to view them from the outside is inviting a break-in. The best, IMO, would be to use a delivery-van-type, no windows. Inside, bolt down the bikes to the floor using the same mounting/locking techniques available for pick-up truck beds. Next best thing is the THULE Big Mouth. Bike locks to the clamp, clamp and tray locked down to the roof rack, and roof rack is locked to the car. Not fool-proof but better than most external bike transport types.
http://www.bikeforums.net/showthread.php?t=65511