Ubuntu One storage is not encrypted with a user cryptographic key
Like Dropbox, Ubuntu One store is not encrypted with a special passphrase. Therefore, it would be technically possible for someone to get access to your data, either by an untrustworthy employee or by a security breach. See this bug report about UbuntuOne storage data encryption it is still a wishlist.
So I would not synced my ~/.ssh folder to the cloud. Unless you set an encrypted container which is then sent over to the cloud, but then for ssh keys, it is not always that handy. But I give you still handy ways of encrypting your data:
Ubuntu One is using encryption for the connection (as said in the fact), it means that basically the data are transmitted over some sort of HTTPS. You can use a really well done animation of what is visible to eavesdropper when using HTTPS, courtesy of the EFF (Electronic Frontier Foundation).
By clicking on the HTTPS button on the EFF animation, you will be able to see what is visible to everybody when you put your SSH keys in a Dropbox or Ubuntu One container. As the animation tells, many persons at site.com (e.g. one.ubuntu.com) would be able to view your data (and many more). Even if you would use something like Tor to route all your traffic, it would still mean that people at site.com can access the data.
So you have to encrypt the data before it leaves your computer. So it arrives encrypted at site.com with credentials they don't know about. Of course, you would have to use a strong encryption mechanism so that it would make it extremely slow for the people at site.com to crack it.
Of course in case of a bank, you can not encrypt your money, as you pay the bank to handle it for you. So you have no choice but to trust the bank to make their IT system as secure as their physical vaults so that only a small subset of employees (the ones managing your account) can view and modify your data.