Knowing that atoms exist doesn't mean the universe is made of atoms

A relationship doesn't automatically work both ways. If you know what an atom looks like, you know what the universe looks like from a certain angle or in a certain state. But that doesn't mean the same thing the other way around: that the universe is made up of those particles. The arrow in the relationship only points one way, not the other. If you look at it that way, at that depth, it looks like that. But if you don't look at it that specific way, it doesn't look like that. Saying that the universe is made up of atoms is the same as saying that the entire universe is made up of bricks because you've seen bricks in houses.