Encrypting your backup
Under the iTunes Backup option in iTunes is an additional checkbox to "Encrypt local backup." You might think this is unnecessary if you're the sole user of your PC and it is safely in your home.
But checking this box allows iTunes Backup to save all of your account passwords from your iOS device. Without this, you'll be able to restore all of your apps, data, and settings, but you'll have to re-enter all of your passwords — many of which you probably entered once months or years ago and promptly forgot.
Encryption is even more critical if you also use your device for work and keep sensitive company information on it. Encrypting the backup will protect it from unauthorized access and ensure that nobody else will be able to restore your apps and data to a different iOS device.
The best choice: use both together
There's no denying the convenience of being able to back up and restore your iOS device without having to use iTunes or a PC, but it shouldn't be your only method. For the best protection, use both backup options. Take advantage of iCloud Backup's ease and reliability, while also performing a more comprehensive iTunes Backup at least once a month. You'll have the peace of mind of knowing your iOS data will be there when you need it.
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