Bzzz Wrong, I have thousands of Fleet Marks on my various toons and I've never belonged to a fleet. you can get them in a lot of places the give out fleet marks along with Rep marks.
While this holds true for the Defera Invasion, you cannot get marks from the PvE queues unless you are in a fleet. The Devs have said that they want players to earn Fleet marks for grouped play (which is ONE of the reasons Fleet Marks were removed from the Foundry Daily). I would not be surprised to see the reset of the ones that you can so via solo play to be removed.
As far as the OP is concerned, it just depends on the missions you run as to IF you get Fleet Marks or not. Maxvitor reminded me that there is the Defera Ground mission that awards Fleet Marks however, if you are doing the PvE Queues for Fleet Marks then you should not be getting any as you are not in a Fleet.
Fleet Commander in Chief for Covenant of Honor [FED] (formerly Task Force A.W.O.L.)
House Leader for Honorable House or Mor'gue [KDF]