(Using iOS 5 and Xcode 4.2.)
I\'ve followed the instructions here: http://developer.apple.com/library/ios/#documentation/UserExperience/Conceptual/LocationA
The best way to do it, would be to subclass MKMapView and override the drawRect method call super, then paint over the map with the color you want. Then each time the user moves, drawRect should respond by drawing appropriately.
MKMapView
drawRect