You’re unlikely to be able to take a rental car between islands. Very few suppliers allow their vehicles to be taken on ferries, and when they do, the renter is usually liable for any damage to the car while onboard. You can find this information for each specific car in the Geographic Restrictions section of the Rental Conditions.
You should never take a rental car on a ferry without the permission of the supplier.
In the rare cases where taking a rental vehicle on a ferry is allowed, it usually is subject to an additional fee (which won’t include the ferry ticket).