The long and the short of it is that the ascendancy of the word Prussia over Brandenburg was the result of two interrelated processes. The Hohenzollern Elector of Brandenburg inherited the Duchy of Prussia in 1618, when it still was a fief of the Polish crown. The Hohenzollerns then began a process of gradually stripping away this Polish authority in the Duchy and expansion of Hohenzollern territory and prestige. Eventually, Emperor Leopold I allowed the Prince-Elector Frederick III to assume the title King in Prussia, a title that was nominally separate from his HRE title in 1701. Leopold I gave this title, which was not really his to give, as a reward for Brandenburg's imperial service. Frederick had been clamoring for a regal title for nearly twenty years by this point and Leopold I granted it lest his Hohenzollern subject take matters into his own hands. Frederick III/I's successors, Frederick William I and Frederick II (aka Frederick the Great), would on their own accord begin to style themselves as Kings of Prussia.
This styling was part of the gradual strengthening of the HRE states by their respective rulers vis-a-vis the Reich and its institutions. Part of this was through acquiring territory or new titles. Hanover's Elector George, for instance, became the King of England in 1714 as well as gaining new territories such as Bremen. Titles had a prestige factor that conferred both leadership and independence within the HRE. Nor were new titles a mere caprice or vanity for these ruling houses. An enhanced and recognized title was a reflection of a real increase in political power in the various HRE structures such as the Kreis. The Habsburgs also played a role in this process, conferring or confirming new or expanded titles as a means to control the process. Nor did new titles immediately supersede the older ones. Frederick III/I remained the elector of Brandenburg and his successors did participate in the matters of the Reich when it suited their interests.
But enhanced titles were not just a matter internal to the domestic politics of the HRE, they also signified a position within European affairs. This was crucial for the ascendancy of the Prussian regal title as bother Frederick-William I and Frederick II tacked to an independent course in their foreign policies. This was crucial because "Prussia" was a title nominally independent of the Reich and its interests. Just as the Hanoverians styled themselves as British monarchs in international affairs, so too did the Hohenzollerns present themselves as Prussian. Frederick II's dramatic successes on the battlefield, as well as his noted antipathy to the political culture of the Reich, helped further bolster the prestige of the Prussian title throughout Europe.
But not all this prestige was martial in nature. Frederick II's military career was in actuality quite spotted and although Frederick-William I built up the royal army to a high standard, both quantitatively and qualitatively, Prussia was still the least of the great powers and needed a larger coalition partner if it were to be successful in its wars. Cultural patronage and courtly life played a role in elevating regal status. Part of Frederick III/I's angling fr regal status was the establishment of the Berlin Academy of the Arts and the Academy of the Sciences. The attending cultural costs of newly-minted kingship was also one of the reasons why few of Hohenzollerns' contemporaries ascended to a simultaneous regal title. Kingship was an expensive proposition for a prince of the HRE; not only did a potential monarch have to spend enormous capital- real and cultural- to gain the title, but then had to spend time to keep it.
Although the Elector title died with the HRE in 1806, Brandenburg remained as an administrative state for the Kingdom of Prussia. Among the numerous titles of Hohenzollerns, they were still Margraves of Brandenburg. But the period in which the Hohenzollerns gained the regal title was also the period some of the Hohenzollern's greatest triumphs. As such, the name Prussia stuck.