Frequent Urination, Burning Sensation During Urination. Have UTI, Bacterial Vaginosis. Taken Cipro. Further?

I am a 47 year old female. On February 18th a saw a doctor because of frequent urination and burning when I urinated. I was was treated with Macrobid for 3 days although my urine culture came back negative for a UTI but positive for bacterial vaginosis . At the time, moderate amounts of microscopic blood was found in my urine and I had a fever of 99.8. On March 3, I was still having urinary symptoms. This time white blood cells were found in my urine and I had a fever of 99.7. My doctor put me on Cipro 500 mg for 5 days and said I had a low colony count but treated it as a UTI anyway. After I finished day 5 of Cipro, I went for a follow up appointment. This time no white blood cells were found in my urine but a trace of blood was. My fever was 99.7. Unfortunately, I am still having frequent urination and burning when I urinate. My doctor is not convinced this is a UTI and has referred me to a urologist. Any ideas on what it may be? Obviously my fear is cancer or an autoimmune disease.