The App Store is Apple's private property. As much as we disagree with its policies of mentioning Any Mobile OS Which Shall Not Be Named, we must allow Apple to do with its own property as it sees fit. This is the essence of liberty. As a developer, you are also at liberty to choose against developing for iOS if you disagree with Apple's policies.
Historically this hasn't been a hurdle for litigation. However, the floral language I used isn't only a result of the App Store - it arises from the many instances of this type of behavior. Take the interaction between iTunes and iDevices as another example. Want to use Winamp to manage your music? Tough. Want to get apps from another store? Tough. Want to browse your phone files with your OS native file manager? Tough. Want to develop apps for the device on anything but a Mac? Tough.
Other companies were litigated for merely pre-installing software on their OS (even though alternatives could be installed at a later date). In many cases with Apple alternatives aren't a possibility whatsoever (unless you violate DMCA).
Microsoft had a monopoly on OSs for PCs, so they were not allowed to use that to give another piece of software an advantage. They did not simply have a monopoly on Windows users.
In order to be regulated under Anti-trust, Apple would need to have a monopoly on some market that isn't simply described as "their customers". The closest they came was iPod, but it looks like that hovered around 75%
Microsoft didn't actually have a monopoly; they got dinged for trying to create a monopoly by strong-arming OEMS that wanted to sell Windows with their PCs, but there were plenty of non-Windows-centric manufacturers (Apple, Sun, SGI, Be, etc.) and plenty of alternative operating systems, even for IBM-compatibles (one of which is now dominant in pretty much every realm other than desktop/laptop PCs).
