The cloud is more than just storage, but usually people use the storage functionality for this.
Realistically, the cloud needs to be treated as another storage medium, just like optical, tape, floppy disks, HDDs, SSDs, and everything else. You plan for media failure, and you build in anti-compromise measures.
The cloud is the same way. If you are an enterprise, you turn on encryption in NetBackup or other program, create a storage pool, and have a mirror on other media (be it an Avamar, a tier 3 disk, or a LTO-6 silo.)
If you are a home user, you encrypt your cloud backups, either by storing things in an encrypted container (TrueCrypt, BitLocker protected windows image, Mac Disk Image, LUKS, PGP Disk volume, etc.), or using a backup program that encrypts. At the worst, there are utilities like BoxCryptor which act similar to CryptFS and map an encrypted layer on top of the cloud drives. Any of this is better than nothing.
Of course, with encryption comes the major bugaboo -- key management. You may have the data securely stashed on the cloud... but without keys, it will be inaccessible. I like having several printed out physical notebook with keys in it, as well as archive grade optical media, and a USB flash drive. Each copy of the notebook goes with a key person (corporate officer), and there is one kept in the local tape safe. This way, if the data center gets completely flattened, it may take days to weeks, but data is still recoverable. This also helps if there is an audit or motion of discovery.
The cloud has its big issues... but treat it as its own piece of media, and it can come in handy. To be more specific, treat each cloud offering as its own media. Amazon Glacier is great for long term archiving, but one needs to well index it, to minimize the stuff retrieved, and Glacier should be the absolute last resort if data is needed, due to the charges for fetching data.