This is correct. Zip provider by default is registered for protected modules. Actually for modules that take care of this by themselves. What you would need to do is to registed your module within VirtualPathProviders. Place this somewhere inside your module:

public class ModuleZipProviderInitializer : IVirtualPathProviderModule
{
    public IEnumerable<VirtualPathProvider> CreateProviders(InitializationEngine context)
    {
        if (context.HostType != HostType.WebApplication)
        {
            return Enumerable.Empty<VirtualPathProvider>();
        }

        return new List<VirtualPathProvider>
        {
            new ZipFileVirtualPathProvider(VirtualPathUtility.ToAppRelative(VirtualPathUtility.Combine(Paths.PublicRootPath, "YourModule")),
                                           "~/modules/public/YourModule/YourModule.zip",
                                           null,
                                           context.Locate.Advanced.GetInstance<IHostingEnvironment>())
        };
    }
}

Thanks for confirming Valdis. I guess they did that for performance reasons.

Frederik