Indoor only cats are more prone to idiopathic cystitis (there are other names for this as well).  Veterinarians don't know exactly why this happens but one of the theories is that a stressful environment plays a big part.  Many of us don't think are cats are stressed.  However, what they see as stressful, we may not or we may not pick up on the subtle things that are stressful to them: children, other cats, dogs, spouses, lack of exercise, lack of mental stimulation.

The Indoor Cat Initiative gives suggestions on how to enhance your cat's environment and decrease its chances of getting cystitis.