Different color theories have been used to determine the ideal colors for different purposes (menus, banners etc.). And the result is that certain colors seem to set standards these days.
No matter which colors became standards, the fact alone that they are standards, is a strong argument for using them.
By adopting standards - the visitors are already familiar with your navigation structure before their brain even recognizes that the page (finally) showed up. That is the point.
For example - some designers play with the idea of removing the browsers back button and replacing it with their own. "Cool!!!", people would say! Yes - very cool, but only from a technical point of view. Not from the users point of view. Why force the user to unlearn what they already know? Why pretend that visitors are as interested in the sites as the authors themselves, when the truth is...they aren't!
It's not important if the designer likes the colors or not. What matters is that people in general like this way of doing things, but most of all, they're used to this way of doing things.
No matter how conservative it may seem to adopt standards - it simply makes things easier for the visitor.
With this being said, there are of course, sites that communicate a message that can't be put into words. Sites that communicate through the uniqueness of the design etc. And of course, what’s written in this article doesn't count for them.
But there are also some web designers that try to re-invent the entire world wide web every time they approach a new site. This might be a charming attitude - but it is rare that they succeed.
Knowing these standards could help you with the colors for your next site. And of course you can differ from the standards.
But in doing so - remember to keep the standards, and their potential benefits, in mind!