The electors of the Holy Roman Empire, and other aspects of the empire's structure, were not finalized until 1356 in the Golden Bull of the Imperial Diets of Metz and Nuremberg. Previously, the method of electing an emperor, as I understand it, was not standardized from election to election, and, in this time period, the House of Habsburg were not yet consistently elected emperor. The house that was relatively consistently elected was the House of Luxembourg. The dissolution of Luxembourg's senior branch did not occur until the 15th century. In addition to having held the title King of the Romans, they also, at times, were kings of Hungary and Bohemia and counts of various counties. In 1356, their power was largely challenged by two houses: Habsburg and Wittelsbach, who ruled both the Palatinate on the Rhine and Bavaria. The omission of Austria from the rank of electors was controversial at the time, due to their rivalry with Luxembourg. Wittelsbach was granted an electorship, but it was not attached to Bavaria (their richest and oldest ancestral lands) but to the Palatinate. This was partly due to Emperor Charles IV's rivalry with Louis IV, who was the previous emperor and was of the Bavarian Wittelsbachs. The Wittelsbachs were not happy with this, as Bavaria was one of the original duchies in the empire and was certainly the primary holding of their house.

It is important to note that the title of Elector came with certain codified privileges and laws. The most important one here is primogeniture. Without this, eventually Bavaria was subjected to dynastic fragmentation. In response to Austria's snub in 1356, their Duke, Rudolf IV, had a forgery made. This forgery was called the Privilegium Maius and was purportedly issued by Frederick Barabarossa himself granting Austria the title of Archduchy. This came along with privileges that suspiciously resembled those of an elector, including primogeniture inheritance.

Of course, in 1526 the king of Bohemia/Hungary died in battle with the Ottomans. The Habsburgs inherited Hungary (or what was left of it) by a marriage contract with the slain King Louis II Jagiellon and the Bohemian nobles elected the Archduke Ferdinand von Habsurg as King. This meant that the Electorate of Bohemia passed into Habsburg hands. The Habsburgs attempted to increase their hold on Bohemia in the next decades, resulting in tensions that culminated with the Defenestration of Prague and the start of the first phase of the Thirty Years War. This was ended in 1620 with the Bohemians' defeat and largely quelled notions of Bohemian autonomy.

In short, they were not Electors because they had not yet achieved the hold on the Holy Roman Empire that they would enjoy in the subsequent centuries and a rival house sought to diminish and contain their power when Electors were selected.

I'm just a hobbyist, so here are my sources. I believe that they are considered suitable, but the professionals here would have a better idea of that. Others also probably have more depth and expertise.

Heer, Friedrich, trans. Janet Sondheimer. 1968. The Holy Roman Empire . New York: Federick A. Praeger Publishers

Pánek, Jaroslav, Tůma Oldřich, et al. 2009. A History of the Czech lands. Prague