There's a desk inside the bus station where you can book an authorized taxi into the city. I can't remember the cost to the historic centre, but think it might have been around 100 pesos. I experienced no issues doing this about a week ago.
Depending on how much Spanish you speak, it could be helpful to have the full address and phone number of your hotel written down for the driver.
Taxis are easy. Verify the fare when you get in, they use a zone system. Inexpensive.
Yes, at the bus terminal you will pay for the taxi chitty at the official desk, show them the address.
I took a local RUTA or small bus into town. it's a ways into el centro but get to see some neighborhoods. 8 pesos maybe. Not as quick but cheap and fun. Let us off right at the Zocalo.
Get em out front a ways.
Thanks for the information.