Amsterdam to Freiburg

I assume you mean Freiburg im Breisgau in SW Germany. It's hard to imagine flying would save you much time, given that you'd need to get to Schiphol airport, arrive an hour early (more?) to deal with security, probably an hour flight, then an hour or more to get into Freiburg. I'd guess four hours travel time if you fly. If there's a direct train that takes six hours, that's probably how I'd go - sure a lot more simple than all of these different modes of transportation. (I do love train travel, though, so it would be fun for me.)

If you can find a cheap flight between AMS and Basel, it will probably be faster to Freiburg than taking the 6 -6.5 hour train from Amsterdam.

Figure this way.
1/2 hour from central Amsterdam to Schipol.
2 hour check in, go through security, walk to the gate, wait to board the plane, then wait to take-off.
1 1/2 flight time to Basel
1/2 hour to get off the flight and get luggage.
1/2 hour waiting for the next bus to Freiburg (average)
1 hour bus to Freiburg.
That is 6 hours city to city. Compare to 6 1/4 hour by direct train. Plus you have the cost of getting to Schipol, then the Flixbus to Freiburg (about 22+ EUR), and if Easyjet, extras for checked luggage and seat selection. Easyjet is 64.60 EUR on Sept 15. Sparpreis ticket is 100 EUR for that date.

Thanks everyone for responses! We've decided that flying is out due to check in, security, etc. We're going to train to Cologne; spend a few hours there and then train to Freiburg! Fun :)

there is only one non-stop train, approx. 6 hours duration.

Train is the best, fastest and most comfortable way to go.
There are NO non-stop trains. There is a direct train at 07:02

Amsterdam Centraal dep 07:02
Utrecht Centraal dep 07:36
Mönchengladbach Hbf dep 10:05
Köln Hbf dep 10:55
Siegburg/Bonn dep 11:09
Frankfurt(M) Flughafen Fernbf dep 11:52
Mannheim Hbf dep 12:36
Karlsruhe Hbf dep 13:00
Offenburg dep 13:28
Freiburg(Breisgau) Hbf arr 13:59

There are lots of other trains later in the day taking similar times that require changes. Do not restrict yourself to direct trains, changing trains is no problem.

You might also want to check out whether there might be more things to do in much closer Cologne (for example) than there are to do in Freiburg. (I would certainly say that Freiburg is a better outdoor-activity destination than Cologne.) Note that hotels in Freiburg are not able to offer the free KONUS local transportation card to guests, as can many other Black Forest destinations.