Debian systems need to enable mod_rewrite manually, as the ServerRoot is non-standard

INSTALL.txt

@@ -156,8 +156,12 @@ you can place include that file in your apache.conf/httpd.conf. We
 prefer the former. In other systems there are similar ways to accomplish
 this. Consult your OS's documentation if unsure.
 
+If you are on a Debian-based system, you will also need to enable the 
+mod_rewrite module manually.
+
 Shell commands as root::
 
+ a2enmod rewrite
  ln -s /var/aegir/config/apache.conf /etc/apache2/conf.d/aegir.conf