Would it not be reasonable to assume that once the Dutch navy had been demolished, that British/French/Spanish troops could just steamroll over their colonies?

It is, and it's exactly what happened to the Dutch around 1800. The fourth Anglo-Dutch war (1780–1784) had been a disaster for the Dutch navy and several colonial holdings had been seized by the British. Because of French support they were returned in the treaty of Paris.

In 1795 French revolutionary armies entered the Netherlands, from that point on, until Napoleon's defeat the Netherlands was firmly in French hands. Naturally, this meant conflict with the British. The fleet still had not recovered and was in no position to protect Dutch shipping or colonies. Over the course of the revolutionary/Napoleonic wars virtually all overseas possessions were occupied by the British. The only exception i can think of is Dejima, a tiny island in the port of Nagasaki. But since that was only rented from the Japanese it doesn't really count.

So why did the Netherlands still have huge a colonial empire well into the 20th century? Well, the British returned the Caribbean and Indonesian colonies to Dutch control after the wars. Why? I'm not quite sure, perhaps they were afraid to bite of more than they could chew, perhaps they wanted to keep the Netherlands as a counter to France. They held on to the Indian ones, Malakka and the Cape though.

Bear in mind, Dutch territory in Indonesia was a lot smaller then than it was in 1940. The reason they were able to keep and expand this colony was basically that the British let them. For example, originally the Dutch were not supposed to expand north of the parallel running through Singapore. But after striking a deal, involving the transfer of the last Dutch African colonies to British control, the demarcation line was changed, and the Dutch expanded into northern Sumatra, against fierce local resistance.

As for the Portuguese, well, the reason their Asian colonies were limited to Goa, East-Timor and Macau is that the Dutch and British took the rest during the 17th century. The Dutch East India company tried seizing Macau in 1621, but failed to take the city.

EDIT: sorry or rambling, i'm not a great writer.

Note that the land area actually controlled in Portugal's eastern trade empire (Brazil being a far different story) wasn't that extensive -- much of it was composed of small defensible fortresses that gave them disproportionate influence over local trade.

I think the question needs to be turned around: why did the small countries do so well early on? Even before the fall of Constantinople Portuguese sailors were exploring the coasts of Africa thanks to advances in cartography, navigation and the development of the Caravel.