That was along the lines that I was thinking. Once there is a rise in passengers (say about the 20-25% level), there may be delays as a result of the severe capacity limits being imposed to maintain safe distancing. That wouldn't be an issue on longer distance services where seat booking is mandated, but commuter lines are almost exclusively used by walk-up passengers who might actually be late for work etc., if refused boarding. In ordinary times, they would either squeeze themselves on of claim that the train was too crowded, - not necessarily getting payment in those cases.
There might be a case for some season ticket holders to receive a pre-agreed partial reduction based on the per-journey figure costed into the tickets but other than that, non-frequent travellers I suspect would have to take the inconvenience on the chin.