www.idos.cz tells you all you need to know, and it is in English (press the English button - the one with the Union flag).
It is a long journey - about 13 hours, and costs approx. 78 Euros. There is one direct train a day - 0753 from Prague, arriving at 2123.
Otherwise there are several changes involved, or change in Vienna at the very least.
I wouldn't get the bus, especially in summer, as it would get very hot and cramped. It would be cheaper, but you get what you paid for :) I don't know where you would find that information - possibly www.eurolines.cz
The bus only takes 11 hours and costs about 1200 Crowns (about 50 EUR), but it only goes once a week on Fridays, leaving Prague at 9pm, and arriving at 8am the next morning. The plusses are: It would save on a hotel for the night, it wouldn't be very hot, you can book online at www.eurolines.com. minuses: miss out on scenery, might be a bit cramped.
Actually your choices through Vienna seem limited as well. If you want to get the train, then you should get the 0611 JOZE PLETNIK to Zidani Most and then change to the Zagreb train arriving 1814 - it does take 12 hours, so take a couple of good books. You can buy the tickets on the day of travel, or a couple of days before if you wish. You can't book on-line, but I wouldn't worry - there will be very few people going that distance - here's a layout of the train www.vagonweb.cz/razeni/vlak.php…
(click on 'foto' for a picture of the interior)
AS for flying - most people will want to fly to the Croatian coast, so most flights are to Split, Dubrovnik, Zadar, etc www.skyeurope.com unfortunately, as you have discovered, the national carriers are very expensive.
Hope this helps!
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