12 Days Germany, Austria, and Switzerland

Try Bahn.de, which is the official site of the German railway system. You can find out about schedules and tickets there, and they have an English option.

Zürich to Frankfurt travel is mostly within Germany and trains there offer advance discounts on a limited number of seats. You may want to go ahead and commit to a date and time to save money on that ticket. The search engine will show you both the current Savings Rate and the Flexible/Full fare at the same time.

Bought in advance tickets at the above-mentioned site of the Bahn are considerable cheaper. For an ad random date end of August the trip can be as cheap as EUR 59,90 (instead of EUR 115,90) if you don't mind to commit yourself to a specific train (day and hour). The process is simple: payment by credit card and your ticket as an e-mailed pdf.

Did you check to see if you can buy an open-jaw ticket and fly home from Zurich, maybe for no extra money?

If you already bought the tickets, make sure you can check in for your return flight 3 hours before departure, travel-time wise. As you know, if you miss the flight, it will be very expensive to get home.

me and my wife are traveling to these countries in 2 weeks. At the end of our trip we need to take a train from Zurich to Frankfurt and fly home.

If you are flying home, you don't want a train Frankfurt, you want one to Frankfurt(M)Flughafen, that is the airport station. Trains from Switzerland call at either Frankfurt(Main)Hbf (the station in the city centre), or Frankfurt(M)Flughafen, but not both (different trains). Be sure you look up the correct station on https://www.bahn.com/en/view/index.shtml and get the correct destination.

And buy from abovementioned DB website, they are the company running the trains. And buy in advance to save money. You get a print-at-home ticket from the website.
Are you actually starting from Zürich, or somewhere else in Switzerland. If you are not starting from Zürich city centre, then enter the actual place you are starting from in your search, not Zürich.

make sure you can check in for your return flight 3 hours before departure
Sensible warning!
I hope you don't plan to go directly from Switzerland to Frankfurt airport to get your flight. The slightest mishap on your train journey can result in missing your flight. I just had it on a train journey from the Netherlands to Germany. Problem with a freight train on the track. Three hours delay. Back from Germany to the Netherlands some accident. More than one and a half hour delay.

What about taking a $200 Lufthansa flight from Zurich to Frankfurt?