We have seen atoms in many ways. Some of them are very indirect.
Large microscopes that use electrons instead of light have been able to see
single atoms as fuzzy pictures on film. The atoms we have seen this way are
the larger atoms that contain a lot of protons and neutrons in their nuclei.
A very good question. The answer is Yes. And No. The reason
for No is that it is actually impossible for anybody to "see" an individual
atom, since all atoms are thousands of times smaller than the smallest light
waves we can see using our eyes. The reason for Yes is that, even though they
cannot be seen directly with our eyes there is so much evidence for atoms, and
we know so much about them, that it is impossible to say they do not exist.
One of the greatest achievements of the last few years (which won a Nobel
prize) was a new kind of microscope called the "scanning tunneling
microscope", which allows an extremely sensitive "probe" (basically a rod with
a very fine tip) to wander around on the outside of some solid materials, and
actually feel the bumps that are caused by the atoms there, and then a
computer can convert those bumps into a picture of the surface, showing the
individual atoms lying there, and the patterns they form, the steps as one
layer of atoms gives way to another, and all sorts of details that could never
be seen before.