Exactly the reason most bugs are now resistant to antibiotics. Unless his doctor cultured and verified he had a bacterial infection or the signs and symptoms were classic for such an infection there is little reason to ever prescribe them.
They can fuck with your own gut bugs too - at least some can. Ciproflaxin is one of those super broad spectrum types that will destroy your gut flora and that can cause problems on its own (including discomfort and gas and other nasty stuff). I think his doctor is a complete retard actually. I don't think he did more than 'oh your stomach hurts, sometimes bacterial infections cause that... here's a broad spectrum that will kill these type of bacteria' and that was about as much thought as was given.
Forget that viruses are far more often the cause of this type of illness.
After you have a smoke, go and eat some probiotics as well. I'd consider stopping the antibiotics completely unless you have a diagnosis that needs them. If you do have a diagnosis (meaning they cultured something, which it sounds like they did not) then make sure you finish as prescribed. Otherwise you're just throwing good money after bad.