Prostatitis, varicocele and cysts (intra-testicular or in the epididymis) are all potential causes for pain, but all tend to present somewhat differently. Prostatitis can cause pain deep in the pelvis but does not typically present with pain in the scrotum; it can cause symptoms related to a urinary tract infection
such as increased frequency of urination and burning with urination; in young patients that are sexually active this is often due to an infection with gonorrhea or chlamydia. In older patients, it is typically caused by the same bacteria that cause common urinary tract infections. If you have been diagnosed with prostatitis (through a combination of urine studies and physical exam), then you may require up to 3-4 weeks of antibiotics to eradicate the problem.
Varicocele and cysts are diagnosed by ultrasound as you have had. Varicoceles are caused by engorgement of the veins in the scrotum, and typically cause a dull aching pain in the scrotum itself; this pain may improve when laying down. Cysts are usually not painful unless they grow to a significant size.
If you are still having pain after treatment with your antibiotics, then you should seek further care from your primary care physician
for further work-up and treatment.