For what reason private ferry operators can charge lower fares than subsidised operators for similar crossings.

In line with current competition law, private ferry operators have commercial freedom to set their own fares. The fares of subsidised operators are generally regulated by the authority providing the subsidy.
There are a small number of cases where a “similar crossing” is served both by a subsidised operator and an unsubsidised operator. In these cases there are also important differences. The subsidised routes are longer, as they have a particular socio-economic focus, for example to provide a link between town centres. Subsidised routes also tend to serve established ports with higher berthing and traffic dues. Subsidised operators are required to deliver a range of public service obligations enshrined in public service contracts which do not apply to purely commercial operators.
In practice, current fares on these routes are comparable. For some fare categories the subsidised service is cheaper; for others the unsubsidised service is cheaper.