Eventually, every cyclist ends up transporting his bike with a car. There are four ways to do this that I'm aware of. And after using all four ways extensively, I can say with some confidence that there are serious pros and cons to every choice. I use all four ways depending on the logistics, practicality and type of trip. Is the car full of family and gear? Will I park in a busy/crowded downtown area? Will I park in a garage? Am I going long distance at high speed? Do I already have other gear on the roof or on the trailer?
From what I have seen, more bikes are damaged more severely while being transported than while being ridden. So choosing the proper way to carry your bicycle is a big deal in my book. Here is what I know about the pros and cons of each method that I have used:
On the roof

| Pro | Con |
|---|---|
Totally out of the way. Takes up no cargo room, doesn't get in the way of cargo access. |
Subject to abuse from flying debris - insects, birds, rocks, twigs, dirt, rain, hail - all the stuff that chips the paint on your hood, and your windshield. |
Harder access for thief |
Must lift bike overhead - hard to reach |
Looks cool (apparently) |
Biggest hit on gas mileage |
| Carry multiple bikes on small cars | Biggest danger: Driving the car under an overhang - garage, carport, etc |
| Won't work on convertibles | |
| Bike is invisible; can't check on it by glancing out the window | |
| Must install cross bars on the roof - often involving paint abrasion |
In the car
| Pro | Con |
|---|---|
Hardest access for thief |
Consumes all cargo room |
| Best protection from the elements | Can get hot enough inside the car to pop the inner tubes |
| No gas mileage hit | Gives a reason for a thief to break into the car - usually damaging the car |
| Bike can be petted while driving | Grease, mud and skid marks on the car's interior |
| More bikes means a bigger car is needed |
On the back of the car (hitch/spare tire/hatch mount)

| Pro | Con |
|---|---|
| No lifting of rack or bike | Easy access for thief |
| Most aerodynamic for exterior carry | In the way of cargo access |
| Well protected from the elements | Your bike is now your rear bumper. Parallel parking and reversing puts the bike in harm's way |
| Bikes visible through the back window | |
| Fastest and easiest rack and bike mounting and removing |
Trailer

| Pro | Con |
|---|---|
| No lifting | Easy access for thief |
| Aerodynamic | More weight for the car to pull |
| Protected from flying debris | Dealing with trailer at destination and when backing or parking. Requires new driving skills. |
| Totally out of the way. Takes up no cargo room. | Storage of the trailer at home |
| Carry the most bikes, including BIG bikes | Most complicated preparation |
| Drop your "bike rack" at destination and use the car unencumbered | Most expensive option |
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