The following converts the coordinate to a CGPoint in the polygon view and uses CGPathContainsPoint to test if that point is in the path (which may be non-rectangular):
CLLocationCoordinate2D mapCoordinate = ...; //user location or annot coord
MKMapPoint mapPoint = MKMapPointForCoordinate(mapCoordinate);
MKPolygonView *polygonView =
(MKPolygonView *)[mapView viewForOverlay:polygonOverlay];
CGPoint polygonViewPoint = [polygonView pointForMapPoint:mapPoint];
BOOL mapCoordinateIsInPolygon =
CGPathContainsPoint(polygonView.path, NULL, polygonViewPoint, NO);
This should work with any overlay view that is a subclass of MKOverlayPathView. You can actually replace MKPolygonView with MKOverlayPathView in the example.
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