Yes, forgetting to tag off sucks, but a conspiracy to nickel and dime you? Really?
How exactly is caltrain a monopoly? And if it is one, fares pay less than 50% of their revenue, with a large fraction coming from government grants. So it would be a government supported monopoly on those tracks, where a private service is probably not cost effective.
So be glad that the government is subsidizing keeping you off the 101.