The ferry runs all day from Chiquila (6 am, 8 am, 10 am, 11 am, 12 am, 2 pm, 4 pm, 5 pm,Last ferry = 7 pm) I haven't done the bus from Merida to Chiquila, but have taken the bus from Cancun to Chiquila and back quite a few times. Very comfortable and no problems. The ferry dock is next to the bus stop in Chiquila.

You can also contact your Holbox hotel and they can help with arranging a driver from Merida. We did this when we stayed at Miwimbi and it was very reasonably priced ($65 USD pp for 2 people) from Cancun airport all the way to the hotel doorstep). We did this going to the island the first time we visited because we just weren't sure of what to expect. After that we did the bus thing, because the bus is much much much cheaper.