How to backup Airport Extreme USB drive with Time Machine
Time Machine is only designed to backup internal and locally-attached drives. It cannot backup network-attached storage devices (such as the AE-USB). If you would like to backup this network drive you will need to look at another software solution capable of doing so. Some recommendations would include Carbon Copy Cloner and ChronoSync.

Another thing you can do is purchase an external hard drive capable of RAID 1 configuration. While this won't protect you from accidentally deleting a file, it will protect you from hard drive failure.