Brunel saw no reason why the GWR sphere of operations should stop just because the tracks stopped at a port! His vision was that the rails would stop at Bristol, Plymouth, Fishguard, Birkenhead etc. but that the GWR would take passengers on to places like New York via ships such as the ‘Great Britain’.
More parochially, as the GWR grew and reached the extremities of the west coast, it became involved in ferry services from Weymouth, Plymouth, Fishguard and other ports where its trains terminated. To explore this fascinating if less well known aspect of GWR history, it may be best to start with the Wikipedia page which provides a good map and general overview.
For a more in-depth look at the ships operated by the GWR and its associated companies look here.