Well we do see atoms, and we see them directly -- in the sense that atoms are a direct cause of our perceptions.

However what "seeing atoms" means at a "given resolution" differs.

There's a long history of this paranoid game: we think the stick is bent! We were wrong! We didnt see the stick at all ! (false).

Ah, but damn: how is it now we know we were wrong? How is it now that, when we took the stick out of the water, we know it isnt bent?

Every sceptical example ever posed has this feature: it presumes that it is possible to be right. That is quite daming to the whole project of scepticism; it is, essentially, incoherent.

Without the possibility of knowing the stick is bent, our mistake was never even a mistake. The very worry of being mistaken is a worry which presumes that truth & knowledege are the ordinary background of our experience.