There can definitely be a difference in price depending upon whether or not you arrived on a flight. This isn't necessarily Hertz's fault; these localities levy taxes based on this distinction so that they soak people who have no ability to change the law. If you price on Hertz.com as "I'm not arriving via plane" then you can get the lower rate. There may or may not be consequences of doing that. I'm not sure just turning up via the shuttle means you pay the higher rate, but certainly they won't be holding you a car for a late flight or anything like that.

I booked a car at SFO that way, and the price was lower because I avoided a tax based on those arriving by flight within 24 hours of the rental in its case, if I remember correctly. I didn't lie. I had arrived on a flight 3 days before and arrived at SFO that morning by BART. I book all my PIT rentals that way, but it doesn't appear to make a difference here.

Even when these are listed as "fee" or whatever they can be related to tax. I think at PIT I always pay "Concession recovery fee". This would appear to be related to a high fee or tax charged the rental car companies at the airport, as opposed to a tax charged directly to the renter. I suppose it's possible some of these could instead be build into the price of the rental, but there's probably competitive pressure there that keeps them listing it separately.