The main creators of the myth of the "Dark Ages" were the men of the Renaissance and Enlightenment. The philosophers, scientists, writers, and politicians during the early modern period (roughly 1500-1800) looked back on their past as a time of ignorance for a couple reasons:

1. The influence/dominance of Catholicism and religion. This is especially true of countries where Protestantism would come to dominate the landscape. England especially was proud to renounce their history of "poper" that had kept the people in ignorance during the medieval period. A central idea of the sixteenth century Reformation was that the Christian Church had become corrupted after the first few centuries and became a dark and superstitious institution with a false idol (the Pope) at its head. The goal then for many reformers was to return to the style of theology and worship held by the early Church fathers.

2. The revival in ancient studies. While any Medievalist will tell you that most intellectuals of the medieval period were familiar with the ancient Romans and Greeks, the early modern historians and philosophers disagreed. Erasmus of Rotterdam, for examples, was one of the leading intellectuals of the early sixteenth century, and one of his main arguments about how to improve society was to go back and read the wisdom of the ancients. He was also a firm believer in reading and understanding Scripture, but that's not the point here. Erasmus argued and persuaded intellectuals to adopt a new style of education called Humanism where students would be immersed in Latin, Greek, and even Hebrew in order to properly understand both Scripture and the teachings of Aristotle, Plato, Sallust, Cicero, etc.

3. The conflict between the Catholic Church and "Science" was played up in the enlightenment era as two diametrically opposed forces. The loss of great architectural pieces, like the aqueducts that littered the Roman Empire were seen as indicative of the failure of Medieval society. Part of the problem with the interpretation of loss is that these ideas simply were not lost. Charlemagne built a gold lined dome in his palace at Aachen in the ninth century. The areas under the influence of Islam from the ninth to the thirteenth centuries had masterful architectural works in their cities. The problem for Europe was that the loss of the great urban center of Rome, and the growing influence of Constantinople and Jerusalem meant that the capital (money) was leaving Europe and prevented the sizable investments that these buildings required. The other problem with the loss hypothesis is that most manuscripts of ancient authors are from the ninth to the eleventh centuries. The modern edition of Sallust's Bellum Catinlinae has about a dozen manuscripts of the ancient work, and all are from the medieval period. The works simply weren't lost.

Finally, the enlightenment that solidified this idea of decline also held the people of the past to an unreasonable standard. This was true of the Victorian historians as well. The writers would hold ancient or medieval people up to the intellectual standards of the society the writers were living in. Enlightenment historians would look back to try and find reflections of their own society in the past. One famous example are the heretical group in England known as Lollards. They were originally a group of elite English lords and theologians who followed or were affiliated with the teachings of John Wycliffe. The group posed a political thread in the 1380s but after that they were rarely ever a coherent body again. However, periodically through the next 150 years, Bishops would find people in their dioceses that endorsed Lollard principals. These should look familiar: Confession to a priest was worthless; the Bishop of Rome had no more power than other Bishops; the Bible was true work of scripture and that all the succeeding writings were misguided, etc. Enlightenment (and many earlier) historians took these persecutions as evidence of a "God's chosen people" persisting through time until the true Reformation. This is just one example among many possible where people of the Early Modern era cherry-picked their examples to prove the decline of the Medieval era or the rise of their own time period.

Sources: Thompson, The Later Lollards; McConica, Erasmus; McConica, English Humanists and Reformation Politics Under Henry VIII; Meri, Medieval Islamic Civilization: An Encyclopedia, esp. pp. 60-65; Marshall, Reformation England 1480-1642.

There are some great posts about this topic in the FAQ here.