I live in Berlin and while there are sometimes disruptions, it's hard to complain when the interval between trains is 4-5 minutes. Just get on the next one. Actually, if the train is 2-3 minutes late, it makes sense to wait another 3-2 minutes after that because it's guaranteed the late train will be crowded, and the next one will be undercrowded, because most people don't follow this principle.
Sibling comment says all traffic in Munich is funneled through the same central section; that's also true for several Berlin lines, but I've never heard of it becoming a problem. Maybe one time. Berlin's network[1] is complex enough that you have plenty of alternate routes available if something like that happens.
Note to future urban planners: a ring railway is a great idea as it provides redundancy of any possible route through the city center. (Very large cities might even need two. The Soviets actually built a second ring to avoid West Berlin, but it doesn't run as a continuous service. You can see various regional services running around the very outside of the network map.)
I've also traveled fairly long distances by regional train (yay Deutschlandticket) and by ICE (absolutely worth it if you're not penny-pinching). It's always disrupted; trains are always late. But I always get to my destination, so I don't mind that much. If you're on a nice and relaxed schedule, like traveling the day before, you'll be fine. It seems an acceptable, despite not ideal, way to run a railway network.
I think that unlike plane travel, where you normally get there exactly on time but there's a small chance you might be seriously delayed, with German train travel you're quite often a few hours delayed (for a cross-country trip) but it's never worse than that. You never have to stay the night in a hotel, you never have to pay extra money to get rebooked, and you never have to sue them afterwards. IIRC, if you're estimated to arrive more than 20 minutes late, you're allowed to just hop on any train towards your destination - the DB app will tell you this - and you don't need a new ticket, though it's recommended to get a note from a customer service desk to prove it occurred.
Note that the German network runs a lot of trains on a lot of tracks - unlike, say, the French TGV network, which has dedicated tracks for TGVs. The German approach allows for more services with less reliability and the French approach provides the opposite. AFAIK, there are a lot more ICE routes than TGV routes because the routes can be pieced together from existing local track segments and incrementally upgraded.
Side note: I've been on a regional train that was delayed 10 minutes, then sat on a siding for another hour to let more important traffic such as ICEs run on schedule past it. There is a tradeoff between resource utilization, and slack which allows for quick return to equilibrium. The more timeslots are occupied, the longer it takes before a delayed train can find a normally empty timeslot to fit into. This also applies to computers.
And people have been complaining about train delays since long before I got here.
[1] https://sbahn.berlin/liniennetz/