I flop my top back on when I can, but I usually flip it back up at night simply to keep the dew from getting on everything. I don't have a garage so it is exposed to the elements. that's fine for some, not for me. I hate getting dressed and getting a wet ass from a damp seat, even though it hasn't rained. I live in the country so I don't have to worry about people stealing from me. If they do, it's not going to be something out of my Jeep. If I lived around others, I would definitely put my top back up over night. Even if no one is going to steal from you, they could flip a cigarette in or do something else that's damaging.
I usually will leave my top down anywhere I go, but I have had my favorite CD stolen while in a store. It doesn't prevent anything, but it does make it much easier for someone to walk by and grab as opposed to taking the time to break in. If you have anything worth much, your's will be hit first due to ease of access.
Also, Lock your consoles and glove box.