I'm going to say what I always say.
Firstly, ENCTS reimbursement- it isn't a subsidy, it is payment for services- is calculated from a starting point largely based on the single adult fare. Therefore there is a perverse incentive for bus operators to have very high single fares for short journeys, which most of them do. It's only when you look at day and weekly tickets that you start to get fares that are not distorted by this.
Secondly, ENCTS only reimburses for the passengers who would have paid, not everyone who travels. This has an effect where operators have to increase capacity to accommodate ENCTS passholders but do not receive additional income to pay for the increased capacity. Notable examples include Arriva Teesside having to convert the X93 to double deckers because of ENCTS passholders, and Yorkshire Coastliner having to get rid of their single deckers because they couldn't cope for the same reason. This means the additional capacity has to be paid for by fare-paying passengers, leading to inflation.
Thirdly, ENCTS reimbursement rates are falling because of significant and prolonged cuts to council budgets. DfT no longer contribute towards the cost of ENCTS, and the councils' central formula grant funding has been falling for the last seven years due to austerity. This means that bus operators are getting less money for carrying the ENCTS passholders, a revenue stream that they cannot control, therefore the shortfall inevitably has to be made from increases in revenue streams that they do control. That means farepaying passengers.
There are also the other costs that bus operators have that increase and, again, they can only cover the shortfall from revenue streams that they do control. This means that, in areas with a lot of ENCTS pass usage, fare rises have to be much higher than inflation just to balance the books.
The essential problem is that the government have precisely no intention of funding the ENCTS reimbursements properly, but they lack the political courage to abolish what is an unaffordable freebie.