In this case the train only takes about 40 mins longer than driving Prague-Berlin- 4.5 hours vs 3hr 50 mins per google maps on a route with tolls. If you buy the train ticket far enough out it can be as low as 25 euros. I just did the train again in January. If you have to fly into Tegel, that means a bus ride into the city, and time to claim baggage, so figure how much time you'll need for everything from the trip to the airport to security to being there early for boarding and you may find you're not saving that much time overall. Just hasn't made sense for me to even think about flying when the train is so convenient.