Well you can try to find a cheap flight...ot you you could look at the big picture...
Berlin to Amsterdam is about 358 miles (576 km) (311 nautical miles)
Train from Berlin to Amsterdam 7 hours + 1 Hour for prep time boarding some waiting and what not =
8 hours (maybe)
Flight from Berlin to Amsterdam 1 1/2 hours + 3 hours arrival before flight leaves + 1 Hour for delays/security related issues + 1 hour pre-arrival issues/baggage pick up =
6 1/2 HOurs
If ya break it down your not saving as much time as you think, i learned that first hand. If you can find a cheap flight...go for it, but if you are paying an arm and a leg just take the train, the scenery is better!