The type of assumption that only an atheist would make is something like, "science can potentially answer any question". Science is merely a way of drawing conclusions. It gives itself certain limitations, so that it can more efficiently answer the types of questions that it is designed to answer. Science has a structure. That structure defines what falls within the bounds of science and what does not. If you study the structure of science on your own you will find what does and does not fall within the bounds of science. The question of the existence of a deity does not fall within the bounds of science regardless of whether that answer is affirmative or negative.