1548 is very much before the era of English naval pre-eminence in Europe. English or British dominance in the Atlantic only really became established at the end of the 1600s.

Prior to this, English monarchs occasionally had a successful naval policy, particularly Richard I, Henry V and Elizabeth I, but just as often flawed royal policy or political turmoil left the English unable to project much power at sea. Many English monarchs, up to and including Henry VIII managed the navy as a temporary organization that could be used to support and transport the army. The English Channel was to them a highway rather than a moat. English naval institutions, meaning cannon foundries, dockyards, drydocks, ties to the merchant community, pay and victualling apparatus, and so forth mostly got their start in the Elizabethan Era (1558-1603) and barely existed in 1548.

Moreover, in 1548 the English royal government was in the hands of a regency following the death of Henry VIII and lacked the political organization to make sure that naval and military responses were coordinated and a coherent naval strategy was followed. Given the history of English seapower prior to 1548 and the current political situation in 1548, a clumsy naval response isn't all that surprising. Only the rise to dominance over the next two centuries makes it seem so to us today.

Sources:

Rodger, N.A.M. The Safeguard of the Sea: A naval history of Britain 660-1649

Loades, David The Making of the Elizabethan Navy 1540-1590 From the Solent to the Armanda