We did this about 18 months ago, + cenote swim. It was way too far from Progreso. The ride was 30-40 minutes longer than advertised in each direction, Chichen Itza was packed, super dusty with wind blowing the dust into our faces, and the group was too big to be able to hear the guide say anything. The parking lot was an absolute ocean of tour buses. The entry was so crowded all I could think about is when you hear about people getting crushed in a crowd.
The Cenote was beautiful, cool and refreshing, amazing. I loved that part, except how much we were rushed because of how long the drive and crowd delays at Chichen Itza had been. We had 40 minutes at the Cenote, and that was supposed to include changing, rinsing, swimming, drying off, and eating lunch, and being back on the bus. We were back to port around 5:45pm, and I think the ship was supposed to leave Progreso around 4:45pm. We were lucky and had 2nd dining. A lot of people were scrambling to get to dinner.
If I were at that port again, I would chose smaller ruins in closer proximity to port, or probably I would just do a cenote swim, also closer to port.