James
You are being very kind to the airlines; "justification" is not the word I would use!
The Passenger Load Supplement, for example, was never and still isn't a "Tax" under any definition. It's simply a variable charge by an airport for the use of its expensive facilities, without which the airline could not operate.
Calling it a "Tax" merely concealed the fact that the airlines started adding these charges to the quoted fare, instead of paying them from within the quoted fare as they had done since the 1950s, as a means of increasing their revenues by about 20%.
This happened at about the same time as all the regional airports started being sold into private hands by their local authority owners, in the late 1980s and early 1990s.( In the UK only what are now the BAA airports were ever state-owned until that damned woman sold them; aside from military ones, of course.)
So the notion that their charges could be called a tax because the airports were state-owned is misguided for several reasons.
The reason that some airlines grudgingly add the words "and charges" to the word "taxes" is because calling any of these charges a "tax" was always a lie, and they were forced to admit it. Even now, they try to give the impression that most of it is some kind of unavoidable tax. It's not. A lot of it goes straight through to restore the airline's bottom line to health. See Ryanair accounts as an example.