RoutePrefix vs Route

Route prefixes are associated with routes by design in attribute routing.

It is used to set a common prefix for an entire controller.

If you read the release notes that introduced the feature you may get a better understanding of the subject.

ASP.NET Web API 2

Attribute routing

ASP.NET Web API now supports attribute routing, thanks to a
contribution by Tim McCall.
With attribute routing you can specify your Web API routes by
annotating your actions and controllers like this:

[RoutePrefix("orders")] 
public class OrdersController : ApiController 
{ 
    [Route("{id}")] 
    public Order Get(int id) { } 
    [Route("{id}/approve")] 
    public Order Approve(int id) { } 
} 

Attribute routing gives you more control over the URIs in your web
API. For example, you can easily define a resource hierarchy using a
single API controller:

public class MoviesController : ApiController 
{ 
    [Route("movies")] 
    public IEnumerable<Movie> Get() { } 
    [Route("actors/{actorId}/movies")] 
    public IEnumerable<Movie> GetByActor(int actorId) { } 
    [Route("directors/{directorId}/movies")] 
    public IEnumerable<Movie> GetByDirector(int directorId) { } 
} 

What’s New in ASP.NET Web API 2.1

What’s New in ASP.NET Web API 2.2

A really good article on the subject

ASP.NET 5 Deep Dive: Routing

While no expert on the subject, here is my understanding of how this works.

With attribute routing the framework inspects the route attribute on the actions of a controller in order to create route entries to add to the route table. So as long as you are using attribute routing you are going to be using the [RouteAttribute]. Without this attribute the action will default back to convention-based routing. The RoutePrefixAttribute is an extensibility point that allows you more control of how you define your routes/Urls. The release notes say as much.

Other than my understanding and the last link provided, everything else was quoted from MS documentation.