I think its a case of German law makers thinking: If it looks like a taxi, and acts like a taxi, then it should be regulated like a taxi. Can't really fault them on this.
The bigger issue is that Uber, Lyft, etc. are trying to take advantage of the lag between what is available (Hail a taxi via an app), and what the current incumbent do now, by bypassing the current laws. This is admirable from a competition perspective, but not by sacrificing all laws to get there and compete.
Uber is notorious at this point for operating full steam ahead, against regulation, and even court rulings, to get into place. I am not surprised Germany took a dim view of their antics and slapped them.
Some regulations are in place to protect drivers, others are in place to protect passengers. To declare yourself immune to them all is lovely, but its as effective as me declaring myself King of the Internet and demanding all my subjects to send me $5.
Adding "with the help of a mobile app" to the end of your business plan, does not suddenly make a brand new industry and to pretend otherwise is delusional (except to shareholders or venture capitalists).