I keep mine covered with the top down if there isn't much rain in the forecast. One thing with these is that if you get enough rain, it will pool right over the driver and passenger seats because of the rollbar shape.
That happened to me in an unexpected thunderstorm, then I had the cover leak when I tried to get the water out of there (I pulled the cover and the weight of the water caused it to leak at a seam).
I bought the Smittybilt cover when I first got the Jeep and was unaware that much of their stuff is of questionable quality.
Its about 90% waterproof, but I'm no longer comfortable leaving the Jeep covered with the top down after getting wet carpets during a couple of big rains. It was less than $100, and it seems many of the better waterproof covers are more than double the price.
Someone on the forum made a PVC bow to keep the water from pooling over the center. Thats a great idea and addresses the main issue with covering a JK with the top down.
Oh... I also wanted a full cover, not just a trail cover. Those get mentioned a lot, but if I have it covered anyway, I'd like to prevent sun damage as well as rain protection. My Jeep isn't my daily driver and sometimes sits all week.