In "civil disobedience," what war does thoreau say made him distrust governments ability to rule justly

The answer is: Mexican-American war

At that time, government's involvement in Mexican-american war met with a lot of resistance from large portion of american citizens. Despite this resistance, the government choose ignore the people's will and initiate the war anyway.

In civil disobedience, Thoreau argue that his distrust the government ability to rule justly because by paying taxes, the government basically violate the free will of its citizens by forcing the citizens to contribute to the war (the taxes are allocated to military budget)

sounds good to me mate!