Mainly because they weren't technically Spanish. They were one of the possessions of Charles V/Carlos I, King of Spain and Holy Roman Emperor, but they weren't in any way subject to the Spanish Crown, in the same way that Spain, despite being ruled by the Holy Roman Emperor, was not part of the Holy Roman Empire.

Charles inherited overlordship of the Low Countries from his father, Philip, Duke of Burgundy. His claim to the Crowns of Castile and Aragon came from his mother, Joana, who he was co-monarch with after his grandparents' deaths. He won the election to be Holy Roman Emperor, and thus had theoretical overlordship of most of Germany.

However, each of these dominions was a separate entity, and was only connected to the others by its ruler. When Charles abdicated his titles, he split his empire, which by that point stretched from the New World to Germany. Partly, this was due to its sheer size making it impractical for one man to rule. Partly it was also to avoid the unrest caused by using one part of his realm to finance the problems of another; Spanish gold funded Charles' wars against Protestants in Germany, and in return Charles spent most of his time outside Spain.

The western part of Charles' dominion went to his son, Philip II. This included Castile, Aragon, the New World, and the Low Countries. The Holy Roman Empire went to his brother Ferdinand. The Spanish Low Countries retained their culture, but were ruled from the Escorial near Madrid by Philip. While they were still not technically subject to the Spanish Crown, this distinction was essentially academic, and this was one contributing factor to their rebellion, especially since Philip was unwilling to accept toleration for Protestants in the Low Countries.