In general and this applies to most of Europe to greater and lesser degrees, while there is much more of a usable passenger rail network than there is in the US (for various reasons), that doesn't mean you can travel pretty much anywhere by train. There are swaths of countries that have very limited train coverage so it depends on where you want to go. This is true elsewhere also. Japan has a great train network in general. But that doesn't mean, for example, you can necessarily get to more rural and mountainous areas by train.
In the case of the Czech Republic, I've never noticed an issue but then I've only needed to travel between Brno and Prague or Vienna.
Yeah, major cities in Czech Republic are fine, smaller ones are much more spotty and you need to really plan beforehand if you don't want to get stuck somewhere on the road till the next day.
Agreed that even in Japan it's not perfect in the countryside, but definitely much better than here in Czech Republic at least based on our two three week trips so far to Japan.
Trains are usually barier free EMUs/DMUs, stations are clean and have amenities, mostly stop at markers so are easy to locate even on big stations and are basically always on time. Like, there is not even a place to show a delay on the station signage usually!
With Czech trains its very rare if it arrives on time, often the platform is only reported a couple minutes before arrival and might change if the delay is too long. Then the train arrives at random part of the platform and people trying to get in or out fan out around the carriage doors. Once you climb on board up a couple steps from the platform to the train, you can expect more delay to be accumulated as you travel. Also the toilets on the stations might often be an "xperience".
In the case of the Czech Republic, I've never noticed an issue but then I've only needed to travel between Brno and Prague or Vienna.