If you’re suffering from inflammatory symptoms like prostatitis, you need to remove the source of the inflammation. The fact that anti-inflammatory drugs provide relief should be enough evidence that this is something worth pursuing. Rebalancing your gut flora can go a long way to reducing inflammation, but it’s only part of the solution. Try reading these articles. Dietary changes, exercise and vagal nerve stimulation, as well as getting your vitamin D serum levels up to a healthy level will all be important in finding a cure.
Taking antibiotics is going to cause you unpredictable long-term problems that are extremely difficult to overcome, even if they provide temporary relief. The drugs are also going to irritate your GI tract and throw things even further out of balance. Try to start implementing changes ASAP to save yourself further unnecessary suffering.