There were a lot of political changes at the end of the 90s, some spurious arguments were made, also saying „it would be too expensive“, despite having a huge history of building train stations and airports for much much more then the planned costs … this was just an excuse to not build it because they did not want it.
They said the passenger estimations were too high and it would not be profitable. Today this route is the most used one in Germany with 17000 passengers per day and a capacity of 8.7 million per year[1].
Transrapid (already the model TR08) would have been able to reach the destination in way under 60 minutes, including two intermediate stops. The ICE was able to do this in 90 minutes (when the reconstructed track was finished in 2004), but today the scheduled duration is 104–110 minutes. Also the track is shared with local trains.
[1]: https://de.wikipedia.org/wiki/Bahnstrecke_Berlin%E2%80%93Ham...