Most people visiting San Diego can pick up their hire car from Lindbergh airport just outside the downtown area, and a car is essential for getting around, as you'll have to drive quite a lot. Cheap car rental in San Diego is easy to arrange but you need to make sure that the rental agreement allows you to take it across the border to Mexico if you plan to visit Tijuana.
If you don't want to drive around the city, then there are pretty good bus services, and also taxicabs with meters meaning that there is no need to agree a fare before you set off.