Traffic Commissioners could withdraw or amend licences, but only with reasonable cause; hence the establishement of a statutory appeal process. The issue is not whether an incumbent bus operator had 'goodwill'; but whether such goodwill attached to a right to pick up and set down passengers at states along a particular defined bus route (over and above the ownership of their buses and depots). After 1930, road serivice licences provided exactly that; they guaranteed that the operator could not legally face direct competition along a defined route, and such licences did indeed feature as assets in operator accounts (as counterpart franchises do today in London, and may do in the future in Manchester).
You would recognise, I am sure, that if a transport authority were to contract with an operator other than an incumbent franchisee, to run bus services on a route covered by the franchise; then the franchisee would have a case in law for compensation. Equally, a franchisee can sell on their franchise to another operator. Once both of these rights applied to holders of road service licenses; but after 1985, they could not. Generally, if legislation abolishes the asset value associated with an activity, while leaving the activity itself still happening, there are clauses in the legislation for disposal of those assets - or otherwise provide compensation. But if, as in this case, there were no such clauses, the legal effect is simply to tranfer all that asset value back to the Crown (since the Crown is legally the fount of all value, in the first place).