Some people are more susceptible to the side effects than others, so you have to pay attention to your own response. But keep in mind, ALL medications have potential side effects. When you read the label of any medication, it can be daunting. Just look at a bottle of Tylenol or cough syrup as proof! And these are things that a kid could pick up at a drug or grocery store. That's not to say some medications aren't potentially more harmful than others, but drug companies are required to list all of the potential side effects, even those which are extremely rare.
I've been on cipro several times, and in fact I was prescribed cipro before and after all of my surgeries, and I was also prescribed it for a bladder infection a few years ago. I can't report any problems with cipro; I seemed to do fine on it. Though, I did have some unpleasant effects from flagyl, another antibiotic prescribed for pouchitis. This was mainly feeling very tired with loss of appetite the entire 10 days I was on it. It wasn't enough for me to stop it, though. And it did take care of the pouchitis, so it was worth suffering through.