http://www.theguardian.com/politics/2014/oct/12/rail-privati...
Great research by the author there. Private operators have a market share of 25% urban/regional transport in Germany, ie. those railway routes that are co-financed by the public. The biggest private operators are French and British. As long as I don't have to buy a special ticket when I ride their trains -- and I do ride them all the time --, it's all the same to me.
The point is, if you want to take the train, either book ahead (and maybe get a BahnCard 25), or get one of the other two. I used to do a mere 2h journey a bunch of times a year (as returns), and the BahnCard 50 easily paid for itself in just 2 or 3 trips, while also offering fantastic flexibility, since it's always 50% off the regular price, which is static.
That's how people afford trains. Also, with the BahnCards, you usually get a free ticket for central public transport zones at your destination, for example for Zone A in Berlin.
Just for your example, a single from Munich->Berlin costs 65€ with a BahnCard 50, i.e. 130€ return, booked right now. The booked ticket lets you ride at any time within the next two days, so you are also not tied to a specific train and it's no big deal if you arrive later at the station etc. (which is not the case for special offers, which tie you to a specific train). 130€ return from München Hbf to Berlin Hbf is really not that bad.