Sir Thomas is sailing out the Tagus River that runs through Lisbon, Portugal. Portugal was then under Spanish dominion, and Sir Thomas has just fulfilled a diplomatic mission for King Henry VIII as the king's ambassador to the court of the Holy Roman Emperor Charles V of Spain. Charles is Europe's most powerful ruler, so this was a stressful assignment.
Sir Thomas knew full well the precariousness of life and favor at the Tudor court, as he had witnessed the rise, fall, and execution of his friend Ann Boleyn. Thomas himself had been a favorite at court and then had spent time in the Tower of London like so many other courtiers.
His poem ends with a call for aid on his voyage to London, the town that Brutus dreamed of, and pleads that his loyalty and love to king and country are his sole reasons for living. This can be read as betraying a sense of anxiety over not just the voyage, but also of his reception at court.
His reference to the legendary tale of the Trojan founding of London reflects his classical education, and Sir Thomas Wyatt along with Sir Henry Howard, Earl of Surrey, are remembered as having introduced the sonnet to England. Wyatt was influenced by Renaissance humanism and especially by the sonnets of Francesco Petrarca.
Note that his subject matter is legendary history, a city, loyalty, the two rivers, the sun, the moon, the symbolic wings. There is no Christian imagery, and everything he mentions would be quite at home in classical Roman poetry.