Most tow bar and boot mounted the bike carriers hold the bikes separately but there's still potential for the bikes to rub together. This will be more likely on a 'hang on' style bike carrier compared to a 'wheel support' rack.
Some people use something like pipe lagging or old towels to protect their bikes. We also sell a range of products that are designed to minimise damage to your bike frames.
Wheel rim protectors are also available to help cushion the wheels and prevent scratches, especially to carbon wheels. These wheel protectors fit onto the wheel straps.