I've been trying to find the operating hours for Zurich transit system but haven't had much luck. I'm sure someone here is familiar with it.
Here it is.
http://www.zvv.ch/zvv/en/home.html
The first S-bahn to the airport from Hauptbahnhof is at 5:02 and takes 12 minutes, if that is what you were wondering about.
MrsEB, the agent gave you the link to sbb.ch because its the central point for ALL transport in Switzerland and every Swiss uses it almost on a daily basis. You can search by tram stops (trains, funiculars and ships are also integrated in Zurich) to any other place in Switzerland. When I used to live outside of Zurich and commute in that was my goto in terms of all things transport. SBB now also has a fantastic app on the iphone that has the same schedules (ie every, tram, bus, train, boat and mountain railway in Switzerland).
Most likely the agent gave you that information because EVERY mode of transport has differing hours (as do the tram and bus lines within Zurich). Some lines are 24 hours, some are more limited - it really depends on the line and it varies widely. Without asking for the specific line, she might not have been able to give you a concrete answer. She might not have been a native English speaker and might not have fully understood your question. There are lots of variables at play here.