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I don’t think there is any absolute way to protect from lightning strikes, especially direct ones. I had one at home and wiring was vaporized. Someone else can explain the concept of good grounding, but it is important to have the ground rods as close as possible to your tower and make sure that it is electrically sound. A good grounding system allows your tower’s electrical charge to vary with that of the earth. By keeping the charge the same a lightning strike is less likely to take place.
It’s hard to protect a transmitter which has to be mounted on the antenna, but you might consider running your antenna lead through an in-line protector. It was designed for CATV, Satellite and TV coax. It probably wouldn’t be enough to protect your transmitter from a direct strike, but it might make a difference if the lightning hit nearby. From my experience even a nearby hit can be devasting as far as damage goes. If you go back through this forum you’ll find some posts about isolating your audio equipment and power leads from your antenna/transmitter. That could prevent a serious injury or even a fire from lightning.