What would become Tokyo did indeed start as a fishing village, located at a strategic crossroads on the Kanto plains. This location would lead to it being fortified, used as a military base, and eventually the base of Tokugawa Ieyasu. When Tokugawa became shogun in 1603, he continued to administer from there, making it the de facto capital of Japan.

Due to its location as regards tectonic plates and nature as an island nation, all of Japan has suffered from various natural disasters over the years, not just Tokyo. I don't believe there's anything to suggest that Tokyo is massively more prone to natural disasters than any other region of the country, especially on its eastern coast.