the database-file can be on the iPad. Backup has to be done via iTunes IMHO (if the database is stand-alone on the iPad, not on a FMServer)
There is an option in FileMaker Go menu on the iPad to Save/Send the Database. This allows you to: Email; Save and Open; Save; Cancel. When Save is selected, a copy of the database file is stored in FileMaker Go.
That said, it is not too secure to store backups on the iPad or iPhone. iOS 5 can delete files from most any app whenever it needs more capacity.