Several points here.
Firstly it's my recollection that this idea of splitting things out from the fare started when duty free was being done away with in the EU. BA, in particular, was worried this would cause airport revenue to fall and that they would then raise their fees to airlines. This, in turn, would cause the airlines to have to raise their fares. The view was that this would cause back lash against the airlines when (in their view) it should be aimed at the airports. IATA then changed the definition of what had been the "Tax" box on a ticket to become "Taxes/Fees/Charges". Trouble is people still refer to it simply as the "tax box".
YQ (and YR for that matter) were introduced to permit airlines to add their own fees. I don't know what they're being used for in this case but typically airlines have used them for fuel surcharges and/or insurance fees using the argument that such fees go up and down and rather than increasing/decreasing fares it's more transparent to leave the fare alone and implement a surcharge.
The business of stripping out various charges has now moved along even further (baggage charges, pillow charges, reservations fees, ticketing fees, seat fees ........) and some of these are shown using the T/F/C box and others are split out on to a separate document leading to further confusion (if you can show some fees on a separate document, why not all?).
In my view, one of the problems is the continued use of two character codes. If, instead of YQ the document given to the passenger said "Insurance Charge" or even "Additional amount charged by our insurer because of the most recent terrorist outrage" (or similar wording if the airline self insures) things would become clearer.