I got actually 2 Groups on my paragon and when one of these 3 is on autofire, my flux will rise.
1. Hardpoint
2. Beam (Short and Long,... this is the group i meant)
Other reasons not to use autofire are:
-There is often more than one enemy ship.
-My Tachyon Lances and Phase Lances need to be timed and fired simultanously to kill (small) enemies in one shot. Otherwise i have to follow half killed ships and waste more flux and time while more enemies gather around me.