While it's true that the soup nazi is actually based on a specific
restaurant in
New York City, it is also
endemic of
lunchtime restaurants in
Manhattan in general.
Picture this--you have probably millions of people on this little island who all need to eat between 12 and 1 o'clock every day. While there are lots of restaurants, there is still a finite number and thus each one needs to serve many people in a short period of time. And yes, New Yorkers are not known for their patience and laid-back qualities. In this case, it's merely a case of needing to get back to work, or eat, quickly.
Thus, restaurants need to serve efficiently, and can't waste time with dawdling customers. It's as simple as that. It's not rudeness on the proprietor's part--to the contrary, they're being polite by making sure slow people don't ruin lunch for everyone else. It's a sort of collectivism where weak links cannot be tolerated.