If traveling by train, you'd need to catch a train first to Warsaw, and then transfer to a train to Torun. There are direct trains from Prague to Warsaw, one in the day, one overnight. (Perhaps there will be extra train services put on for the Euro 2012 matches, but the rail carriers have not yet released any information about that.)
We should expect that the prices for flights to Polish cities will be extremely high in June, the same with Polskibus (which also has direct connection Prague - Warsaw), so perhaps the only reliable transport with stable, reasonable prices will be railway these days.
Train will be the best or Polskibus.com (the low-cost buses). Yes the prices will be increased but if booked in advanced it should be fine. Having said that tickets for Polski bus don't usually become available until only a few weeks before. You can get a Polskibus from Prague to Warsaw and then another one to Toruń.
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