Why would a PS prescribe long term use of rifampin and Bactrim?

Your surgeon was trying to avoid the infection getting around your implant and inside the capsule. Once inside the capsule, the antibiotics cannot penetrate well and you develop a bad infection, a chronic infection, and/or a capsule.

Your surgeon was most likely trying to avoid an infection from developing. That said, it's best to ask your surgeon for her/his rationale for prescribing the medications for that long.