Crete boasts around 300 days of sun per year. Most of the rain and bad weather occurs in the winter months but there is still a possibility that you will encounter a day of rain at other times. Don't panic, there are other things that you can do if you can't lie on the beach.
The main cities and towns on the North coast of Crete offer plenty of sightseeing opportunities, shopping, museums as well as cafés and restaurants and are a great alternative to lying on the beach when the weather is poor.
CretAquarium is a perfect place to visit if it rains. You'll be indoors and out of the rain and wind. But even in good weather it's well worth a visit
The island can still look spectacular in bad weather (and sometimes even more than when the sun shines). If you can't stay on the beach why not rent a car and just drive around, maybe to inland villages or up into the hills.
Monasteries are another good place to visit in poor weather and there is plenty of those spread around the island. The best known are Toplou in the far east of the island, Arkadi is close to Rethymnon, Preveli on the South coast and Agia Triada and Gouverneto on the peninsula of Akrotiri near Chania. Bear in mind that they may be closed around early afternoon.
Crete has thousands of caves and a few such as Sfendoni and Melindoni are accessible to the general public
Crete produces some decent wine and you may be able to visit wineries. There are of course olive oil factories (almost every village has one) but most of the activities around olives and olive oil happen at harvest time which is in winter.
You will come across small museums. These might be folk museums which present traditional life of Crete or private initiatives such as the War Museum of Askifou or the excellent Wooden Sculptures Museum in Axos.
Finally, remember that Crete has a huge diversity of climate and because there are high mountains it may well rain on the North coast and the sun could be shining in the South (or vice-versa although that's less likely). Check what the weather is like in other parts of the island and if the sun shines somethere else just go there for the day.