While you have rightly highlighted the unpopular steps taken in the passenger and freight segments in terms of fares, there is a larger problem in hand for the railways, and more alarmingly, it is not a problem created by the railway policies, but due to external factors.
While the passenger segment has suffered due to dynamic pricing, the hit has been largely in terms of passenger count. For premium trains like the Rajdhani, there has been a marginal increase in the revenue ( though at the cost of number of passengers).
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And overall too, the contribution of the passenger segment is not really high enough to skew the operating ratio in this manner. Also, this particular year, IR saw a 20% increase in passenger reservation revenue, post demonetization for the month of November.
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But a general unpopularity of these measures tends to divert public opinion away from the main problem that the railways is facing, 'The reduction in Coal loading'.