It is good news that the cystoscopy didn't show anything. CT scan is looking at a broader area than just inside the bladder.
Pretty much every test that comes back negative is good news.
With bladders and the urinary system (kidneys, ureters, bladder, urethra, the associated sphincter muscles) there are multiple diagnostic tests to run when something seems wrong.
Some people just have chronic blood in the urine for no known reason. Also could be a virus, an infection (I know she took antibiotics already), minor injury to some part of the urinary system. Some times it happens and then goes away and a reason is never found.
Sounds like her doctor is being thorough, so again, since the doctor already said it is probably nothing, let's just go with that for now unless some test comes back saying otherwise.
Mike