In fact the variance for that very example - Hamburg Berlin - is much higher by car. Finding a parking spot in Berlin can be very tough, and you end up cruising around the neighbourhood for 10-20 minutes. Add another 10 minute walk from the parking spot to your destination.
Traffic can vary, too, and you want to allow significant padding for traffic jams. If I drive from Hamburg to Berlin I’d start 3:30h before my appointment at the destination. With the train, 3h is probably realistic, although there is variance as the train only goes once per hour.
It’s more extreme on the distance Berlin Munich, where taking the train is vastly faster. At night you can max out your car and drive an average speed of 200km/h down the Autobahn (although it’s extremely tiring to do that for hours), and then you can make the distance in 4h by car. During the day, 6:30-7:30h is more realistic. The train takes 3:45; add to that an hour for public transport on both sides.
It’s different when you don’t go to the big cities. You can take the train from Munich to a ski resort in Austria, but it will take twice as long as the car, and you need a cab for the last few kilometres. But nothing beats the train when travelling between large cities in Germany (not even flying, unless you have a private jet).