Although you arrive at the church separately, you most definitely leave together - and that may be in any number of ways. Below is a list of ideas that others have tried.

1. An antique car is a favorite; these may be rented, or possibly borrowed from a friend.
2. Horsedrawn carriages are romantic, although they may be hard to find in your area.
3. A hot air balloon is definitely a unique getaway.
4. A fire engine has been used to take a couple from the church to the reception.
5. A horsedrawn sleigh could be a romantic touch for a winter wedding, or one at a ski resort.
6. Pedicab - a cart for two which is pulled by a bicycle - is a novel mode of transportation, providing the   distance is not too far.  
7. Boat or gondola, if the ceremony or reception is near water.

No matter how you leave, the important thing is that you are leaving as husband and wife, and on your way to a wonderful honeymoon.