The term "atoms" is a label, used to describe a state of matter which scientists have deduced from experimentation and observation. (Actually, I think they have actually seen the atom, through electron microscopes or something similar, but I'm not sure of it.) It's like using the term "chair" to describe a piece of furniture which is used for sitting. You can call it anything you like, but it's purpose is still the same.
So too with the atom. Scientists are able, repeatedly and quantifiably, to isolate discrete particles of matter which they term atoms. And when they treat these atoms to certain experiments, under certain conditions, they will react in predictable, and repeatable, ways.
This is the difference between science and religion. You don't have to take anything on faith. If someone has achieved a certain result in science, you can achieve the same result by performing the same test. It's not necessary to believe in atoms. You just have to do the experiments yourself to show that they do, indeed, exist.