Got it to work with the following.
Placed this code in the bootstrap.
$front = $this->getResource("frontController");
$front = Zend_Controller_Front::getInstance();
$router = $front->getRouter();
$route = new Zend_Controller_Router_Route('/:username', array('controller' => 'index','action' => 'user'));
$router->addRoute('minipage', $route);
An alternative for this is placing the rules in the config.ini:
routes.router.type = "Zend_Controller_Router_Route"
routes.router.route = "/:username"
routes.router.defaults.controller = "index"
routes.router.defaults.action = "minipage"
;rules for the exception to the above rulles.
routes.indexItem.type =Zend_Controller_Router_Route
routes.indexItem.route = cms
routes.indexItem.defaults.controller = cms
routes.indexItem.defaults.action = index
routes.indexItem2.type =Zend_Controller_Router_Route
routes.indexItem2.route = policy
routes.indexItem2.defaults.controller = policy
routes.indexItem2.defaults.action = index
routes.indexItem3.type =Zend_Controller_Router_Route
routes.indexItem3.route = index
routes.indexItem3.defaults.controller = index
routes.indexItem3.defaults.action = index
And load this from the bootstrap using
$front->getRouter()->
addConfig(new Zend_Config_Ini(APPLICATION_PATH . "/configs/routes.ini"), "routes");