Query custom posts of logged in user only

Create a small plugin to add your custom post type to the default loop, if the user is logged in.

// add custom post type to wp loop
add_filter( 'pre_get_posts', 'fb_add_to_query' );

// ads to query
function fb_add_to_query( $query ) {

    if ( ! is_user_logged_in() ) // if user not logged in, return
        return $query;

    if ( is_admin() || is_preview() ) // return, if in backend or preview
        return $query;

    if ( ! isset( $query -> query_vars['suppress_filters'] ) )
        $query -> query_vars['suppress_filters'] = FALSE;

    // conditional tags for restrictions
    if ( is_home() || is_front_page() && ( FALSE == $query -> query_vars['suppress_filters'] ) ) 
        $query->set( 'post_type', array( 'post', 'my_post_type' ) );

    return $query;
}