I'm looking for the fastest way using the normal public transport options (plane, train, etc.) from Zurich to Eindhoven in Autumn. Flying seems not really to be a option since there seem to be no flights from Switzerland to Eindhoven. The trains that I could find take around 12 hours or even longer and require to change trains a couple of times. The best option I could find so far is flying to Amsterdam and taking a train to Eindhoven, but is there any other option I'm not aware of?
No. The option you mention is by far the fastest. Fly directly from Zurich to Amsterdam. Swiss has four flights per day. This takes 1h30. Then take a train from the Schiphol airport to Eindhoven. That's another 1h30. There are plenty of (direct) trains between Schiphol and Eindhoven. Add the time in between to get luggage, go to the train etc. And you are done.
If you comply to traffic regulations, you won't be faster by car (taxi or rental car) on the Schiphol-Eindhoven leg.
There are also direct flights from Brussels to Zurich. Brussels Airport is a 1h30 drive (by car) from Eindhoven. The train takes at least 2h45 and you have to change 2 or 3 times. Cologne and Düsseldorf are even further apart. Maastricht, Rotterdam and Antwerp do not have direct flights to Zurich.
And this brings us back to Amsterdam ;-)
It's a matter of personal preference, of course, but I'd probably take the train. First airplane and then train sounds like a lot of hassle (check-in, check-out, transport, etc.). Also, you could get into trouble if the airplane is delayed and you miss the train you have booked.
On September 12th, for example, there are various eight hour train connections, but then one has to change at least three times, which can be risky.
However, on bahn.de (screen shot in German), I found one connection where you only have to change twice. Granted, it takes ten hours, but trains should be comfortable (ICE) and you have one and a half hours to kill in Frankfurt, not the worst place.
Don't forget to check other days. September 12th was just a random example of a day in autumn.
One train option that can be quite economical, and save you some time is to take the night train. There is a daily night train from Zürich to Amsterdam. Take that train as far as Utrecht, and take an IC to Eindhoven from there. The "CityNightline" night train has very good deals if you buy sufficiently in advance. You leave Zürich in the evening, and you're in Eindhoven the next day in the morning.