Another way of asking this question is: Why are you so big? If we were smaller ourselves, we wouldn’t think of atoms as being so small. But atoms come in fixed sizes -- we cannot shrink ourselves down and also shrink the atoms down. Smaller organisms are just made up of fewer atoms.
We are complicated beings -- our bodies do lots of amazing things every day. Just to ask a question about atoms requires a brain that can process language and think about what things are made of. This takes lots of reactions among neurons, and lots of supporting roles by other parts of the body to keep it all working. In short, lots of atoms are needed to make a human body as complex and as efficient as it is. It is natural then for us to see atoms as small. A virus typically is made up of far fewer atoms but it cannot ask the question you just did.
If you were to ask why atoms are the size they are given what they're made of, we could answer in terms of some basic constants that influence how the little quantum clouds get held together. But even if those constants were different, you'd still have to put together a huge number of the atoms to make anybody who could ask about their size.