Can you point to a national rail subsidy specific to Manchester after this April? I thought there was no direct rail grant for 16/17 but looking it up seems there is, presumably bridging funding? That's the specific point you are talking about. If you can, then great. But I'd love to know why the huge fare rise was so neccesary in such a short period of time? I note Knutsford to Manchester fares barely increased at all by comparison.
The point you seem to be missing is TfGM set fares were exceptionally cheap at the start of the franchise and there's a franchise requirement for them to be brought in to line with non-PTE fares over the next few years. Greater Manchester passengers will pay more but on average they'll eventually be paying the same as Lancashire and Cheshire passengers. Bridging the gap isn't just about increasing PTE set fares as a few of the most expensive non-PTE fares have decreased.
Knutsford to Manchester increased by the average for non-PTE fares. A few years ago it increased by a lot more the average for non-PTE fares as Northern reduced the less popular Knutsford to Chester fare in favour of increasing the more popular Knutsford to Manchester fare - something new Northern aren't allowed to do.
It does make rail travel less affordable in one of Britain's biggest cities. Why are you convinced that that is not so important, but the high cost of Knutsford to Northwich is?
I didn't mention Knutsford to Northwich. That's actually one of the non-PTE fares Northern have reduced to bring in to line with other fares. It was £5.80 for an Off-Peak Return but was reduced to £5.50 in September 2016. Incidentally the fare on the 289 bus between Knutsford and Northwich changed from £5 return to £5.50 return in the summer of 2016 when the operator changed. The train has the disadvantage of the station being poorly located for the town but has the advantage of being hourly while the bus is a few journeys per day.
I wouldn't call it a cap because if you want to travel all day it still costs more than that unlike with a PAYG cap, which was proposed for Greater Manchester. If that had happened, £5.90 would have been the 'cap', no? £5.40 is the highest CDR fare, that isn't a massively relevant statistic to actual travellers, but if you'd like to call it a 'CDR cap' then that's fair enough.
Off-Peak Return fares from Horwich Parkway:
Lostock (GM) £2.40
Bolton (GM) £4.30
Salford (GM) £5.40
Manchester (GM) £5.40
Stockport (GM) £5.40
Hazel Grove (GM) £5.40
New Mills Newton (Derbyshire) £14.20
So 8.5 miles in GM costs the same as almost 20 miles in GM but go a further 5 miles and cross the border in to Derbyshire and you pay more than double.
Call it what you want but there's a maximum CDR fare when you travel between two points in GM which makes it very cheap to go from one side of Manchester to the other.