Let's hear it for freedom of the press: the clerk is probably the most sensible guy in the whole story. When Kovalev tries to place an ad, the clerk attempts at first to make heads or tails out of Kovalev's crazy story until dismissing the whole nose thing as way too sensationalist for the newspaper's reputation.
But check out the way his reactions are echoed by others later in the story, creating the kind of repetition that ups the dream-like ante Gogol is after.
First, when he hears Kovalev's story, the clerk turns it into something that makes more realistic sense:
"Has a household serf of yours absconded, then?"
"[…] No, indeed! It is my nose that has absconded from me."
"Mister Nose, a Mister Nose? Indeed a strange name, that! Then has this Mr. Nose robbed you of some money?" (2.58-60)
You know who else immediately turns the nose into a person? Madame Podtochina in her letter, where she writes: "I assure you that I have never at any time allowed the civil servant whom you mention to enter my house—either in disguise or as himself." (2.133)
And second, the clerk eventually decides not to run Kovalev's ad even when he realizes that the nose thing is for reals, because
it might injure the paper's reputation. […] only last week a similar case occurred. One day a civil servant brought us an advertisement as you have done. […] all that it seemed to signify was the running away of a poodle. Yet what was it, do you think, in reality? Why, the thing turned out to be a libel, and the "poodle" in question a cashier. (2.67-69)
Basically, he is saying that it's all too TMZ for his paper, which tries to stay away from scandals and stuff. And that's just what the nose turns into: a celebrity hounded by the curious.