The premise of most rainy-day pages does not apply here, so start by replacing it. On Cozumel, rain is almost never what ruins a day. Wind is.
Wet-season rain, roughly May to October, arrives as a heavy 30 to 60 minute afternoon downpour and then stops. It does not cancel diving, because you are already wet and because underwater visibility on this island is set by current and swell rather than by what is falling out of the sky. It does not close the beach clubs. It rarely lasts long enough to reorganise a day around. The correct response to a Cozumel downpour is usually a long lunch.
What genuinely cancels things is a norte: a winter cold front, most common November through March, that pushes hard north winds down the Yucatán channel. When one arrives, the harbourmaster closes the port to recreational craft. That means no dive boats, no snorkel trips, no catamarans, no El Cielo, and sometimes no Playa del Carmen ferry. Closures typically run one to three days and they are announced early in the morning, so your shop will usually call before you have finished breakfast. The second thing that shuts boats down, in any season, is lightning; an electrical storm keeps everyone on shore regardless of the wind.
Here is the honest part. Cozumel's indoor inventory is thin. There is no aquarium, no large museum complex, no cluster of galleries, no shopping mall worth an afternoon. What exists is a small and genuinely good island museum on the malecón, a scale-model park south of town, a botanical garden, the market streets, a handful of tastings and classes, and a town that is perfectly pleasant to walk around in warm rain. If you come expecting a wet-weather programme, you will be disappointed. If you come with a plan, a blown-out day here is easy.
The two best answers to a closed port are counterintuitive and both worth knowing. The first is to go east. A norte turns the windward coast into something spectacular: real swell hitting ironshore, spray over the road, the beach bars half empty and the whole coast doing what it is shaped to do. It is the single best day to drive it, provided you are there to look rather than swim. The second, if you are a diver, is to use the day for theory. Nitrox certification, the classroom portion of a course, or a refresher session are all things dive shops here will happily run when the boats are tied up, and they turn a lost day into a qualification you take home.