Que? That's not how I understand it works. My understanding is that the
bacteria can become resistant to Cipro (much as they can to other antibacterials). If one is being prescribed Cipro repeatedly (highly unusual), it is often for the same bacteria and the odds go up that said bacteria can become resistant. Now, there can be problems if bacteria that one naturally carries around becomes resistant to antibiotics and start causing problems, but that's usually a tertiary consideration when treating a primary infection.
So, let's say you're dosed with ciprofloxacin (the generic name of Cipro) prophylactically for potential [pulmonary] anthrax exposure. If no bacteria are present, then the drug is eliminated from the body in the usual fashion (though side effects can occur, as with virtually every med).
Of course, because ciprofloxacin isn't (barring cultures demonstrating resistance to other meds) the first antibiotic of choice for most infections, it's all mostly moot anyway.