Anecdotally that seems to be the case. The largest burden of this tax is falling on low income commuters who live off the train lines and have to drive into Manhattan, yet all of the money is going to... the train lines (MTA). Understandably they're not too happy.
This is factually inaccurate on so many counts. People who drive into the congestion pricing zone have a higher income than the median in the city. Not only is the number of low-income people who commute by car into the zone is incredibly small, but those people are already eligible for a waiver, so they wouldn't have to pay it anyway.
On top of that, the money is all going to the MTA, but that is not synonymous with "the train lines", because the MTA is also responsible for the robust bus network throughout the five boroughs, and the money raised from congestion pricing has already been earmarked for a whole number of projects, several of which would apply to people who are reliant on buses.