He was made a tempting offer to accept a position in India but the directors of the BNCR recognised Cotton's ability and his value to the company and raised his salary in order to retain him.
Cotton played a leading role in establishing the Larne-Stranraer steamer service in 1862 but it was not a success and closed after 14 months.
He promoted the running of cheap excursion trains and was the driving force behind developing the tourist potential of Portrush where the BNCR acquired its first hotel, Glenariff, and Whitehead.
This practice continued until 1890, when the principle of formal election to the chairmanship was established, a change Cotton accepted with equanimity.
The government appointed Cotton as a general investigator under the Congested Districts Board for Connaught and it was largely due to him that the light railways or so-called "Balfour lines" in these areas were constructed.
He was well known in literary circles throughout the north of Ireland as an interpreter of Shakespeare and was himself featured in one of Amanda McKittrick Ros' remarkable novels, Delina Delaney, as "The Father of Steamy Enterprise".