Hi David,
How were you planning to get to Siena? You can check the schedule at trenitalia.com, but if I remember correctly, the majority of Siena - Rome trains go through Florence (with a few going through Chiusi maybe?) Anyway, depending on your mode of transportation, you may want to go back up to Florence and go directly, or go further south for a cheaper ticket. We were in Tuscany recently with a car. We returned it to Orvieto and were aboard an inexpensive one hour train to Rome within 10 minutes of leaving the rental facility.