The problem is that "honest mistakes" and "deliberate fare evasion" are, in the vast majority of cases, indistinguishable from each other.
As
@jamiearmley explains, the Penalty Fare scheme is really what should happen in all cases as it is the fairest and clearest way of addressing the matter. "You have made a mistake, this is the financial penalty for your mistake". You might not like it, but you can't say it is unfair.
If someone keeps making mistakes and keeps receiving Penalty Fares then that's the stage where the consequences need to ramp up.
Where I start having serious issues is where operators deliberately choose not to operate a Penalty Fares scheme and routinely write everyone up for prosecution. I have very serious issues relating to the behaviour of the likes of Transport Investigations who, because they are a private company, seem to be avoiding the public scrutiny being placed upon Northern in particular. What Transport Investigations do is nothing short of an extortion racket and I sincerely hope that the outcome of the SJPN scandal is that railway companies and associated bottom-feeders like Transport Investigations lose the right to bring criminal prosecutions at all.
Sadly we know that the likes of Transport Investigations will deliberately target the people who they know are largely compliant. People who aren't largely compliant don't pay the bloated and unjustifiable 'administration fees' which generates the huge profits. RPIs will also (sensibly) often back down when someone is aggressive towards them- although this can backfire when there's a revenue block backed up by the BTP.