absolutely go to the Autoprogreso website and choose an excursion. it is a very small and poor town, so some are not comfortable wandering through town but DO NOT hide out on the ship. it would be a shame to miss out on the Mayan ruins or Merida. we chose a short visit to Xcambo, only 45 minutes away and a smaller site because travelling with my 80 yr old aunt, We did not want to sit out a 2 hr drive to some of the (possibly) more impressive sites. we were not disappointed, it was still a great experience. their buses are new and comfortable, the staff is friendly, and it costs a small fraction of cruise operated excursions.
we took a cab (about $12 for 4 of us) to Chankanaab park. I dont care about swimming with dolphins, so we paid about $20/person for entrance to the park itself. there was good snorkeling, beautiful grounds to stroll through, and a tequila place where we were shown how tequila is made and given plenty of samples!
the price of the park entrance is a little high, but it was an uncrowded, peaceful, beautiful day.