The lovely idiots who accuse vaccines of causing issues do so with a sort of ignorant logic, yet they do believe they are correct:
Many vaccines contain the element mercury. Due to the toxicity of mercury, many people instantaneously assume vaccines to be harmful, but this is not the case.
Since the mercury is only a component in many far more complex molecules it is entirely harmless, rendering the arguments of anti-vaccination groups useless.
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Just to support your example of dangerous chemicals becoming harmless in compounds, sodium is highly explosive when added to water. But it's perfectly safe in salt.
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Indeed, and even if it is harmful, there is twice as much in a tuna sandwich...