Internet Explorer didn't have dominant market share; Windows did. You say the problem wasn't that a program came bundled with software, but that was literally the heart of the antitrust action: the government contended that Microsoft was using their defacto operating system monopoly of Windows to give IE a leg up on non-bundled competitors.

> An iPhone without apps just doesn't work.

Sure, but an iPhone without an App Store works fine -- that was literally the way the first iPhone shipped, remember? -- so I'm not quite sure your analogy is a slam dunk here. :)