Yes. All cardholder data is heavily encrypted. PayByPhone adheres to PCI Level 1 compliance and is audited yearly to ensure its compliance with the security standards.
You also have the option of enabling your account with a security PIN.
As an added layer, some of the parking operators (SFMTA, Impark, Metro Parking, and Advanced Parking) have added CVV code entry as a mandatory step to processing each payment in order to increase security further.