You are not alone in wondering why the Netherlands came to occupy such a prominent position between the 16th and 17th centuries. It was a question that baffled/surprised even contemporaries, as KW Stuart observes:

The abrupt rise of a country unendowed by nature to such heights of wealth and power was, indeed, frequently regarded as a ‘miracle.’

No single factor can explain the rapid rise of the Dutch Republic. And to discuss all the factors that supported the Republic's ascent is something that is best left to a lengthy essay (or indeed even a book). That being said, here are a few factors which are central to understanding the Netherlands' (relatively rapid) change in fortunes:

• Catholic dislike of heterodoxy — Catholic (especially Spanish) intolerance/hatred of Protestants (and Jews) encouraged adherents of both religions to take flight. They were skilled tradesmen and craftsmen, merchants and bankers, who took their knowledge with them to their new homes in Switzerland, England and, indeed, the Dutch Republic. Their skill-set proved to be a valuable addition to Dutch economic life. Moreover, the ongoing enmity with Spain forced Dutch traders to seek out unusual trading partners — the Republic became, for instance, a primary hub for the grain trade between the Baltic states and the Ottoman Empire.

• Development of trade networks — Dutch dependence on French grain was shaken as a result of crop failures in the middle of the 16th century, prompting traders to turn to the Baltic for grain. Although there were already trade links between the Low Countries, the Hanseatic League and England, the Baltic region provided the Netherlands with great opportunity. Traders began dealing in "other Baltic products such as tar, hemp, flax, and wood" (Harreld) transforming Amsterdam into a major trading hub. Timber was an especially valuable resource that made the Dutch into the world's foremost shipbuilders. "So efficient was Dutch shipbuilding that France, Sweden, and Denmark had their warships built there." (Sommerville)

• Improved agricultural practices — with the improvement of pumps and windmill technology in the 15th century, the Dutch accelerated land reclamation projects (so-called Polderisation). This expanded arable land and, by the 17th century, had reduced dependence on foreign agricultural products. This permitted grain to be treated as a commodity to be traded, rather than a staple to be consumed upon arrival in the Netherlands. In addition, the Dutch were early adopters of crop rotation, which ensured that arable land was used to its fullest potential.

Sources

• KW Stuart, "The Miracle of the Dutch Republic as Seen in the Seventeenth Century", (London, 1967).
• Donald J. Harreld, "The Dutch Economy in the Golden Age (16th – 17th Centuries)"
• JP Sommerville, "The Dutch Republic in the early seventeenth century"
• J.R. Jones, "The Dutch Navy and National Survival in the Seventeenth Century", in The International History Review, Vol. 10, No. 1 (Feb., 1988)
• Richard W. Unger, "Dutch Herring, Technology, and International Trade in the Seventeenth Century", in The Journal of Economic History, Vol. 40, No. 2 (Jun., 1980)
• Mehmet Bulut, "The Role of the Ottomans and Dutch in the Commercial Integration between the Levant and Atlantic in the Seventeenth Century", in Journal of the Economic and Social History of the Orient, Vol. 45, No. 2 (2002)