The red color you often find in Japanese traditional architecture is called bengara (弁柄), originally imported from China and later Bengal (hence the name), it was first successfully reproduced locally in 1707. A red iron oxide pigment, it is made from copper mining byproducts. 
Bengara, being an inorganic natural pigment is completely safe for humans and animals, no off-gases, each layer adds to the wood and helps protect it against weather, UV light. It is naturally water and insect repellant. It is dissolved before use with shochu: distilled alcohol.
To enhance the insect repellent effects on wood it is common to mix it in kakishibu, which is basically fermented astringent persimmon juice. Bengara is also commonly used in dyeing textiles, and lacquerware (effectively immortal), as well as ceramics and stone ware, glazes, etc.
