Brussels is the "capital" of the EU and has lots of hotel rooms for the visiting bureaucrats from 27 countries. In summer (July-August) "all' Europeans take 4 week holidays ;-) and there is a large surplus of hotel rooms in Brussels at relatively affordable prices.

Amsterdam is a major tourist destination and at peak tourist times (New year's, April/May, during the summer and during some of the bigger conferences) the hotels can easily fill their rooms at premium prices.