When specifying a plugin, you usually have to give the plugin's URL....

$output .= theme('flowplayer', array(
  'clip' => array(
    'provider' => 'rtmp',
    'url' => 'Extremists',
  ),
  'plugins' => array(
    'rtmp' => array(
      'url' => 'flowplayer.rtmp.swf', // OMG WHY DO I HAVE TO DO THIS!
      'netConnectionUrl' => 'rtmp://video1.advid.tv/druptest',
    ),
  ),
));

For the plugins provided by this module, we should automatically fill in $options['plugins']['rtmp']['url'] if it's not explicitly given. This would apply to audio, captions and rtmp.