That's a really good and, I think, deep question.
The main reason is that when we process a transaction, we are doing two things. One is removing the money and, as you say, the work involved in that is pretty much the same no matter what the amount is. Secondly, we're actually writing an insurance policy. The insurance policy is for if there's something wrong with the transaction or if there's something wrong with the product, the good or the service being provided, Stripe will backstop that transaction.
If you go to your card company and say, “Hey, this was deficient. I'm going to issue a chargeback”, or whatever, by default, that chargeback or that dispute goes to the business in question. If the business in question can't afford it or can't refund it for some reason, then Stripe is on the hook and Stripe is underwriting that. Stripe's liabilities actually scale linearly with the transaction amount. That's the reason for the percentage fee.