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)

Detect if MKAnnotation is in MKPolygon

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);