By not flying through thunderstorms. For a small aircraft, the lightning is not the most hazardous part of a cumulonimbus (Cb) cloud system. Mature Cb clouds have huge updrafts underneath them, which can cause enough turbulence to upset most aircraft. Heavy rain and hail is also commonplace underneath Cb clouds. Even the rain can be heavy enough to damage wooden propellers and any components on your leading edge (such as the [leading-edge slats](http://aviation.stackexchange.com/questions/25920/what-is-the-difference-between-a-leading-edge-flap-and-a-slat) found on the Tiger Moths I fly). Hail can put holes in your canvas, which are expensive to repair - if you manage to get the aircraft home at all. This turbulence and rain persists for a much longer period and across a wider area than the thunderstorm itself.

For these reasons, the chief protection against thunderstorms is by training and procedure: student pilots are taught to avoid Cb clouds when they're visible, and to plan flights to avoid areas where Cb are forecast. Weather forecasts and reports specially call out Cb clouds to help with this, and ATIS messages often warn of "cumulonimbus cloud in the vicinity of the aerodrome".

Protecting a wooden aircraft specifically against lightning is not hugely worthwhile, because it's unlikely to be able to stay in the vicinity of the Cb cloud for long enough to be at risk of a lightning strike. It just wooden happen.