The main cause (often somewhat hidden behind the term "decayed infrastructure") is that there are too many trains on too few tracks. There are many reasons for that. I think the main ones are:
* Political pressure to have more trains, without an adequate increase in infrastructure capacity (trains are cheaper than tracks and can be delivered faster). For example, political pressure utterly destroyed the reliability of the local rail system in our area, because the number of trains per hour was increased by a factor of 2-3, with only a minimal amount of new tracks (the majority of the network is still single-track). Apparently, the system worked in simulations under near-perfect conditions (no delays, few passengers, no technical problems). So let's build it! The chaos that ensued during the first few months after the network opened again made national headlines. Another example: the highly overloaded Rhine valley line between Mannheim and Basel was proposed to be upgraded to 4 tracks in 1964. In 1970, the project was scheduled to be finished in 1985. Currently the (ambitious) goal is to finish the project in 2041 [0]. The original line (270 km) was finished after 17 years in the 1840ies.
* On regional and local lines, a tendency to increase train frequency and to decrease train capacity (more trains, but shorter ones). I suspect this is also because of political pressure ("your station now has 4 trains per hour!!"), but it doesn't make any sense. A short train which can hold 150 passengers occupies exactly the same amount of "space" (blocks) on the tracks as a full-length train with a capacity of 1,200 passengers, and they require exactly the same amount of personnel.
* Privatization of DB on the early 90ies, with political pressure to be profitable. Tracks are expensive to maintain, so those parts of the infrastructure that could be classified as "redundant" were dismantled. Now they have a network with little redundancy, which is great from a short-sighted business standpoint, but terrible for reliability.
[0] https://en.wikipedia.org/wiki/Karlsruhe%E2%80%93Basel_high-s...
Train frequency is the most important aspect of transportation. It's probably more important than max speed or even ticket price. A train every 15 min means you don't have to make an appointment because one will be coming soon. At half an hour you will need to study the timetable and plan your life around it.