Unprotected sex is when two people engage in penetrative sex without the use of a condom. Condoms protect against unwanted pregnancy and the transmission of HIV (though not against most other forms of sexually-transmitted disease like syphilis). There are a few other practices that might be considered protected sex (using dental dams when rimming, for example), but mostly people mean putting a condom on a cock when that cock is going into a vagina or anus. The term has nothing to do with safety practices during things like bondage or flogging mean to avoid damaging the sub.