We installed a Maxxair Fanmate 9000 on our rear Fantastic Fan to block any chance of leaving it open in rain downpours (had happened twice, caused by dumb humans both times) and to block sunlight glare when we catch an occasional nap.
The cover we chose is opaque black, does great, looks great on the roof. The FF stays open ninety-nine percent of the time now when we're stationary. If it's really cold outside I might choke it down to a couple of inches, but it's always at least cracked. We had 4 inches of rain on Thu and Fri last week, and it stayed wide open the whole time. Very nice.
We clean the skylight and the other FF with soapy water and a cloth, then spray 303 protectorant and buff it til dry. Works like a champ on the skylight, and not quite as remarkable on the FF cover. But the FF cover is so dark it doesn't matter too much anyway.
Our first skylight was so messed up from water spotting and tree stuff and other gradu we replaced it at 4 years old. Cost us approx $100, I think, for the new one. Took me a couple of hours to replace and I did a heckuva lot better job than original installers did. If you want, you can see pictures and description of the job here