There are several reasons for this.

The concept of an elective monarchy does not mean that no concept of dynastic prestige exists. Prestige was naturally considered a trait that was necessary to be a ruler. The son of an emperor thus had a strong bonus to be elected again. There was hardly a single Roman King or Emperor who did not at least claim to have a dynastically legitimized claim on their throne.

The differences between elective and hereditary monarchies was not as clear as school books or video games make it seem. Laws like the Golden Bull of Charles IV (1356) didn't exist until they were made. In the end, a King became the King through general acceptance by his relevant vassals. Even in France, a country that was ruled by one single dynasty, the Capets, from 987 to 1792, the lay peers lifted the newly crowned King up to his throne during the coronation ceremony. It is coincidence that multiple ruling dynasties of the Holy Roman Empire died out while the Capets never did, or rather, had branch lines left (Valois, Bourbon, Orléans), but this prestigious and factually powerful tradition in France made the monarchy in the end turn out to become hereditary, while the extinction of the ruling dynasties in the Empire again and again damaged the monarchy and put the rulers in a primus inter pares position.

The worst crisis of the Imperial monarchy was the Interregnum after the Hohenstaufen rule (1254-1273). The lack of a central authority allowed princes to occupy royal demesnes. Since later rulers couldn't rely on revenues and possibilities to access territories from royal demesnes anymore (except in Franconia and Swabia where King Rudolf successfully was able to claim a good bit of land back), they had to rely on their very own lands instead, which made it impossible for Kings with not so much own land to rule. When Charles IV began to pawn most of the remaining demesnes, no other dynasty except the Luxembourgs (who ruled over Brandenburg and Bohemia) had an own power base big enough to rule over an empire as huge as the HRE; the short intermezzo under King Ruprecht, the Count Palatine of the Rhine (1400-1410) proved that the rule of the Luxembourgs was effectively without alternatives. The Habsburgs were closely related to the Luxembourgs and inherited their lands.

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By the way, when King Wenceslaus was unseated by the Electors in 1400, they agreed that princes from the following dynasties were worthy to become King:

• Wittelsbach of the Palatinate (the book unfortunately doesn't say explicitly if the Bavarian Wittelsbachs were considered)
• Reginarids of Hesse
• Wettin of Meißen
• Askanians of Saxe-Wittenberg
• Württemberg
• Hohenzollern of Nuremburg

(The Habsburgs and Luxembourgs were excluded for political reasons.)

Reference for this: Jörg K. Hoensch, Die Luxemburger, Stuttgart 2000, p. 215.

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Edit:

In the post-medieval time, confessions started to play a role, and with three of seven electors being catholic bishops and one the King of Bohemia, a Habsburgian territory, they could hardly be contested. The only exception was Emperor Charles VII (1742-1745), a Duke of Bavaria from the house of Wittelsbach, who claimed Austria, Bohemia and the Empire through his wife Maria Amalia of Habsburg during the War of the Austrian Succession.