Yep, mines out 24/7. I originally had a John Taylor cover but after a year or so it lost all it's waterproofing and turned into a useless wet blanket.
I now use a cover from Cover Systems - a local company. It took a while to arrive, but it's proved to be much better than the JT one, and for not much more money. You can go for an uprated two piece cover if wanted, but I've have seen a need and have had no issues with paintwork.
It has some nifty features like door zips, so if you put the cover on and have left something inside, you can just unzip a door and get in.
I tend to keep the roof on from about October to Feb as it rains more often and the rain can pool on the tonneau cover area - however mine is a 4 seater to a bigger surface area.
http://www.cover-systems.co.uk/aboutus.htm