How can I get a train ticket from Vienna/Linz to Cesky Krumlov?

Perhaps use door to door service with CK Shuttle. I can't recommend them highly enough. Safe travels!

There are no trains from Linz to C/K. You can take a bus up to Cesky Budjovice, however. To get back to C/K you would have to switch buses.

It's only about 50 miles from Linz to Cesky Krumlov. There are a number of private transfer services operating out of C/K that can take you relatively inexpensive. They run all over the region from Salzburg to/from Prague, Linz, Vienna and even Budapest. You can spot them on C/K tourism sights.

Perhaps it works with Czech website

https://www.cd.cz/en/eshop/

Found an option by shuttle bus

https://ckshuttle.cz/?aw=3&gclid=EAIaIQobChMIjc2G7I2LgQMVk4KDBx3K6AiuEAAYASAAEgJjDfD_BwE

There are no trains from Linz to C/K. You can take a bus up to Cesky Budjovice, however. To get back to C/K you would have to switch buses.

On the CD website it gives a one change train at Cesky Budjovice broadly every two hours and the CD website given in the preceding post seems to work, in the UK anyway, for ticket purchasing.

Just take the CK Shuttle.

There are no trains from Linz to C/K.

There are no direct trains from Linz to C/K. You must change trains in Ceske Budejovice.

I am trying ... the Austrian website, but having no luck.

The default setting on https://www.oebb.at/en/ is "direct trains only". You must uncheck this option.

The default setting on www.oebb.at is not "direct trains only". That would be rather pointless. Anyway, if you really want to do this by train just buy a ticket at the station.

The default setting on www.oebb.at is not "direct trains only".

Sorry, but this is not true. I had looked up yesterday the connections to C/K and had to uncheck "direct trains only". I just repeated it and "direct trains only" was checked again. (The designers of OeBB's webpages are not the sharpest knives in the drawer.)

Whether or not the Austrian railways website works, if you really want to buy in advance try the Czech railways website referenced several posts above. You can't buy on Bahn.com as no section of the journey enters Germany, which is a pre-requisite to purchasing on Bahn.com.