When I commented last night I was basing my view on what I read in El Reg's article - so I picked up on the word overcharging (unsurprisingly - it's not only used in the article, but the first word of the headline!). However, reading it again, I can see it's not in any of the quoted bits.
Skim reading the PDF, it mentions the longer route used to calculate the users' prices, but doesn't claim the users are being overcharged per se*. So it can be argued that regardless of how its calculated, the amount users are charged is the amount users have agreed to - therefore, they are not being overcharged and it is just that drivers are being underpaid.
However, while the complaint does specify the underpayment, it does also make a nod to the "overcharging" with things like "This fraudulent scheme negatively impacted not only drivers like Plaintiff Sophano Van, and thousands of individual Class members nationwide, but even end users..." which does very strongly suggest that customers were overcharged, without making that the actual complaint.