I thought the same. The second class buses in my opinion are comfortable - not at all chicken and goat buses. However they make stops and the ride can be bumby sometimes. I met a few travelers who took the night bus to Holbosh and they were totally fine with it.

I did make it to Isla Holbosh by way of Cancun. I took a 7am ADO bus from Merida to a bus station in Cancun, then a second class (not sure if Mayab or Oriente line) to Chiquila - then a ferry to the Holbosh.

I was traveling all day, which I did not mind because I really enjoyed the scenery. I checked into my hotel around 5pm that same day.

Good Luck