I am trying to purchase (online in advance for June) on that bahn.de website, a ticket going from Munich to Prague. The total says 108,20EUR. I want to make sure, before I do something really stupid, that this is infact approx. $168 dollars totals for 2 people. Also, it says:
Complete flexibility, refund after the first day of validity 15,00 EUR...
What does that mean?
It appears that you are thinking of going 2nd class, which in my opinion is perfectly ok, and you are looking at one of the three direct 6:01 regional connections through Furth im Wald. There are less expensive ways to make that trip on exactly the same trains.
Buy a Bayern-Ticket for the day of travel. You can get it for €27 from any DB automat in Munich. That will get up to 5 of you from Munich to the Czech border. Also buy a €20 per person Anschluss ticket for the border to Prague at a counter in Munich. Total for two of you would be about €67.
Buy a €32 Bayern-Böhmen ticket. That's like a Bayern-Ticket, but will get up to 5 of you all the way to Pilsen. From there you would get off the train and buy Czech rail tickets to Prague at 143 Krona (less than €6) per person. You might be able to buy the tickets from Pilsen to Prague on the train after you get into the Czech border, but I don't know for sure.
These are regional trains, so there are no seat reservations, either with these special tickets or with full fare.
For the above fares, the Bayern-Ticket is valid all day weekends, but only from 9AM on weekdays. However, the first train, is at 8:44. If that's the one you want to take, also buy two single trip tickets to Freising at €6,60. The train leaves Freising after 9 AM, so the Bayern- or Böhmen-Ticket is valid from there.
And, "refund after the first day of validity 15,00 EUR.." means that if you buy it online (no reason in my opinion, since there are no reserved seats) and you don't use it, they will refund all but €15.