No doubt the government and Southeastern are squabbling over money. The Williams Review has shown that the UK delivers one of the best rates of value for money to the taxpayer in Europe however they seem to always want more and it leads to cheap deals being done and no incentive for the franchise to innovate and invest in the business.
What they mean is pushing fare costs away from the taxpayer to passenger - which increases fares and hurts the poorest. It's not even a reduction in tax burden on a wider level though as the UK then spends many billions in welfare to cover high cost of living (which isn't paid to anywhere near the same extent in most EU nations) where housing, transport and other costs are lower.