That's how it's run most often, my table included. But if it's all just one big undifferentiated loot pile, payers begin to assume that they shouldn't have to pay for anything. The living world begins to disappear, and you risk reducing your setting to "the dungeon" and "the shop."
I guess I like the idea of using these kinds of fees to draw attention to certain elements of the setting. For example, one of the dudes in the comic's comments pointed out an interesting technique:
"The Hell’s Rebels adventure path uses this psychological urge to great effect in building up their villain, the dictator of the city of Kintargo. In the first book (levels 1-3) it is 3 cp to cross the bridge from one side of the city to the other. Inconvenient, but not bank-breaking. The second book (levels 4-6) raises the toll to 5 sp. Also inconsequential to the PCs, but annoying. The third book (levels 7-9) raises it to 2 gp a trip or 10 gp for a day pass. By the fourth book (level 10) the city is open and violent revolt over this B.S. and the PCs take the bridge by force.
"Beyond making the villain hateable, this toll serves the plot function of drawing the players’ attention to the bridge, a key part of the city where they fight quite possibly 4 epic battles over the course of the AP (against a small army of guards, a dragon, the nearly-unkillable dictator himself if certain things happen and a suicide-causing ghost head)."
That's why I think arrow tracking becomes a thing behind enemy lines, and water hoarding becomes a thing in deserts. These details are best when they force players to pay attention to their situation.