I've never heard of antibiotics to clear a cyst / nodule, but then again, I'm not THAT informed, so maybe it is possible.
According to most thyroid nodule web sites, usually the discovery of a nodule involves blood work, ultrasound, FNA, and possibly medication and or surgery, depending on the the size of the growth and the findings.
Try endocrineweb.com. also thyroid.ca for more information, but I"m sure you'll also receive lots of suport from this site.