I would second the opinion about not doing a guided tour, especially if this is your first trip to Europe. The trains between Rotterdam and Amsterdam and v.v. leave every 11-19 minutes and take 65-70 minutes. In four hours, you can see a tremendous amount of Amsterdam, as the tram system is very efficient. I'd take the tram away from the train station a little bit (as some people are put off by the street life), and alternate between walking a little and taking the tram a little. With some planning in advance, you can map out a route that hits a number of key sights, although you might not get a chance to go inside any of the museums.

Brugges is ridiculously easy to do on foot with a decent guidebook. We did it after being on a flight all night and getting into Brussels airport around 11am. It's not particularly complicated.

Actually, I'd probably just spring for a hotel in Amsterdam instead of sleeping on the boat between Zeebrugge and Rotterdam. That way I'd get a nice Indonesian dinner and be able to tour the city leisurely. Depending on how much a guided tour of Amsterdam costs, staying in the city overnight might be cost-effective.