There is a San Diego Trolley station in Old Town San Diego and if you don't have the use of a car, this would be the best way of getting to Old Town.
Depending on where you are staying, take the bus, Blue Line or Orange Line Trolley and connect to the Green Line. The only station that all three Lines connect is at the 12th & Imperial Transit Center. It is located downtown San Diego in East Village. Many of the Trolley Stations offer free parking, some offer only paid parking or street parking. However, if you do have the use of a car and would rather get around by Trolley, listed in the website given below, are the stations and the offer of parking or not.
The SD Trolley is clean and safe and easy to get around on. If you get a Trolley map you will see which buses meet at which stations. The map will also let you know which transfer point would be most convenient for you.
First thing: Old Town Trolley Tours is a tour bus, not the San Diego Trolley--public transportation--which does have a station in Old Town.
The tour begins at Old Town, however you can begin your tour at any of the 7-9 (The number of stops change and at this writing there are 8) stops, because the tour is a two hour narrated tour which goes on an all day loop with on & off privileges.
A ticket for this tour is less expensive if you buy it on-line.