From the report: "the highest income earners contributed to more of the revenue than the lowest income earners, making the scheme progressive in the scale of its equity impact"
It is quite likely that the lower income users are mostly retired people, and students, and they shouldn't be crowding the system at peak times unless willing to pay.
If you price out low-income people, you do get relatively more revenue from high-income earners. But the low-income people also get less service.
The non-charge eligible trips of the low earners declined as well. The paper did not differentiate between sources of income, and I'm not sure how relevant that is.
So the "poor off the zones" stands. Of course it's a matter of opinion whether this is desirable or not.
It is quite likely that the lower income users are mostly retired people, and students, and they shouldn't be crowding the system at peak times unless willing to pay.