The article mentions that the dense network of railway connections in the Czech Republic is result of the focus on economic operation of public transport in the communist times. But I don’t think that there was a special focus on purely local lines and electrification of the railway routes started already after 1945.
The main reason why railway transportation is popular among Czech citizens is very long history of railway transportation in the country - actually the oldest railway route in continental Europe is between South-Bohemian České Buďějovice and Austrian Linz (in operation since 1827). Since the region was highly industrial, it was vital to build dense net of railway connections for cargo transportation, and when the rails and railway stations were built for that purpose, the passenger transportation came naturally along with that. A brief history can be found e.g. here: https://cs.wikipedia.org/wiki/Historie_železniční_dopravy_v_Česku
The high-speed railways were not built in the past because the country is geographically relatively small and high-speed trains would have little use. This situation can change as priority of EU is now replacing air-traffic and long distance car traffic with affordable long-distance pan-European railway routes. But it needs much closer EU-wide coordination both in planning the infrastructure but also in practical operations (e.g. transparent single ticketing system, including a kind of time-based network-wide tickets).