Now vs Later
The issue is that companies, governments, laws and risks change over time.
One might feel comfortable storing all files in "the cloud" now, but how easy would it be to move and/or remove "without trace" that data should the situation change.
A good example might be a smallish cloud based company with good ethics gets taken over by another far less ethical company, out to cut costs and make money any way possible. How secret and secure are your files then?
Even if you deleted your files and closed your account, are those files really gone, or will they still be on there on disk and tape for many years to come.
Hosts of cloud based apps have to make money some how, and If your data is their asset, who is to say they won't keep it until the end of time.