Everyone always forgets about Dordrecht ("Dordt"). In the Dutch Republic, Dordrecht was the second most important city (and port) in Holland, after Amsterdam. Nearby Rotterdam rose in importance later, in the 19th century.

The answer to your question is location, location, location. The ports in the Low Countries were conveniently located between the Baltic (with grain and timber) and the southern European ports (with salt and New World commodities). Furthermore, there's easy access to English ports and the Atlantic if needed.

What happened in the Low Countries is that bulk goods would be bought one in one location, stored at the port, and then sold at a convenient time (when the price was high) at another location (or to a trader from another location). In Dutch this is called a 'stapelmarkt', which is sometimes translated as 'staple market' but a better translation would probably be 'stack market', as it catches the meaning better. Goods would be stacked/accumulated/piled up at the port for resale at a later time.

Once such a system is in place, it reinforces itself. Traders know where to go to buy or sell their goods. If a Spanish trader wants to trade some New World silver for Baltic timber, he doesn't have to go all the way to Baltic and arrange it himself. He can bring his silver to Antwerp, sell it there, and buy the timber there. It's super-convenient. In the 16th century Antwerp became the stapelmarkt in Northern Europe. Which goods were most in demand changed over time, but Antwerp was always the place to go.

This changed during the Dutch Revolt. Antwerp revolted against Spain, but was recaptured by Spanish forces quite soon after the start of the Revolt. This in itself was not a problem for Antwerp as a stapelmarkt, but two other things were. Firstly, the Spanish allowed all protestant people to leave Antwerp (and the Southern Netherlands) for the Dutch Republic. Many traders and craftsmen left for Holland. Secondly, the Dutch rebels controlled the Scheldt estuary. Antwerp is not located at the sea, but is a few miles inland. To get to Antwerp, ships have to pass the 'Western Scheldt', the estuary of the Scheldt river. The Dutch blocked all shipping on the Western Scheldt, blockading Antwerp and diverting trade to Amsterdam, Dordrecht, and Middelburg (all Dutch cities).

So at the end of the 16th century Antwerp was blockaded and the trade went elsewhere. Amsterdam was the main benificiary of this, and soon Amsterdam became the stapelmarkt in Northern Europe. Soon, the position of Amsterdam would be strengthened by the Dutch own colonial trade. During the Eighty Years' War Dutch trade with Spain died down, but this was offset by the VOC (Dutch East Indies Company) and the WIC (Dutch West Indies Company). The VOC brought spices from the East to Amsterdam (and other ports, but mainly Amsterdam) and the WIC raided Spanish shipping the West. The Baltic trade should not be forgotten though. During all this time trade with the Baltic remained the most profitable for the Dutch. In Dutch this trade is called the 'moedernegotie', the 'mother of all trade'.