How to fill hole in slab after installing new closet flange
This is what I ended up doing after some research and opinion asking:

Chisel all the loose concrete edges so there is an undercut. This prevents the patch in the slab from rising. Backfill with sand. As you put the sand in moisten it and tamp it down. Make sure the piping is well supported and that the closet flange is level. Keep adding sand until it matches just below the bottom of the existing slab. Mix concrete and pour into the hole, backing it under the undercut and ensuring no voids exist. Keep filling until it is slightly higher than the hole and then screed it off.

So far it looks okay although I think my concrete could have been a little wetter.