Train: yes, the hub is Aranjuez and you should have to transfer there from the Regional Cuenca-Madrid to the Regional Madrid-Toledo. Considering that the Madrid-Toledo line is under work and trains stop at Algodor and the travellers are transferred there to a bus to complete the trip (20 kms.), I wouldn't use the train in this case.

Buses: AISA is the company that serves the Cuenca-Toledo route. It has two services Mon-Fri at 6:30am, and 4pm, and only one on holidays at 5pm. It takes 2:15 to get to Toledo.