It was from the beginning, as the Crown of Castille had more manpower and was richer than the Crown of Aragon. Despite the Crown of Castille having gone through a very rough second half of the XV century with kings being overpowered by their validos, like the marquess of Villena, Beltrán de la Cueva, and Álvaro de Luna, and some civil wars, Castille was much more populated than Aragon, which meant that Casitlle had more people paying taxes, and also being able to raise larger armies.

By the year of 1482, as per the census of Alonso de Quintanilla, the Crown of Castille had a population of 4.2 million, while Aragon only had 850,000 people. The Kingdom of Granada had some 300,000 people. This capacity to raise larger armies eventually lead to Castille raising regiments to help in the conquests of the Crown of Aragon, most notably the wars in Italy, which saw an important number of soldiers and officers from Castille alongside those of Aragon. Most notably, the commander in chief of those wars was none other than Gonzalo Fernández de Córdoba, the Great Captain, who was from Córdoba. Some notable people that took part in those wars include Hernán Cortés, Gonzalo Guerrero, or Diego García de Paredes aka the Hercules of Extremadura.

Castillian preponderance became much more evident with the discovery and conquest of America, as the riches from the Indies and the management of the whole enterprise was centralised in Seville, through the Casa de Contratación de las Indias. Castille also possessed a poweful navy, experienced in Atlantic navigation, most notably the Armada de Vizcaya or Biscayne Fleet, which was the fleet managed by the Hermandad de las Cuatro Villas (Brotherhood of the Four Villages), that was tasked with fighting piracy, escorting the ships en route to Flanders, and to some extent transporting the goods to Flanders. The commerce of Castille with Flanders was of paramount importance, as it brought in many riches from the wool commerce, that was centralised through the Universidad de Mercaderes de Burgos, and later through the Consulado de Burgos.

All of these factors combined made Castille the uncontested hegemonic power of the Spanish Union, and eventually made Castille be the only one to foot the bills of the many wars, both in soldiers and in cash, even for wars that would have been a matter of the Crown of Aragon.

Sources:

González, Tomás (1829), Censo de población de as provincias y partidos de la Corona de Castilla en el siglo XVI. Madrid: Imprenta Real.

Fernández Duro, Cesáreo (1894), La Marina de Castilla desde su origen y pugna con la de Inglaterra hasta la refundición en la Armada española. Madrid: El Progreso.

García García, Bernardo (1997), Los validos. Madrid: Akal.

Casado Alonso, Hilario (2003), El triunfo de Mercurio: la presencia castellana en Europa (siglos XV y XVI). Burgos: Cajacírculo.

Ladero Quesada, Miguel Ángel (2002). El primer oro de América: los comienzos de la Casa de Contratación de las Yndias. 1503-1511. Madrid: Real Academia de la Historia.