As one whose job is to design/deploy/maintain large scale data center infrastructure, it is by no means a fixed cost. During peak app download times (usually Christmas time to new years) and as demand trends up and down throughout the year, Apple is spinning up and spinning down cloud infrastructure to match demand and save money when possible. Those costs are a function not just of the number of apps in the app store but also the number of active devices around the world, as the number of devices grow so does the demands on the infrastructure.
Also few folks seem to be mentioning the human cost of the app store. I don't know how many people Apple employs on the App review teams, the Xcode Development teams, or on other of the various teams (legal, phone support, etc.) to that work to support the App store, but let's say it's 5,000 people (out of the over 139,000 employees they have) and guessing a fully loaded salary of $300K (salary + benefits + insurance, this is probably a conservative number for California) that's ~$1.5B a year just in human costs.
Not saying Apple still isn't making a lot of money off the App store it's hard to know how much for sure without seeing the real internal numbers, but I think there is a lot more cost that goes in to it than most people think yet that doesn't stop them from judging how much is too much of a fee to charge developers (who by and large seem fine with it).