They aren't and I have. Right now, however, the biggest momentum that the iP(hone|ad) has is the app market, and the fact that a lot of large organizations have special support for its walled garden. 3.3.1 is Apple's way of trying to ensure that it is a specially cultivated walled garden, and that it's more likely that "there's an app for that" only applies to the Apple devices.
I think it's a futile move that is too late, but that is the clearly obvious motive behind 3.3.1. It is anti-competitive and without justification, and honestly it's a bit bizarre that so many fail to grasp that.
Have you considered the possibility that it is not so clear and obvious as you think?
This has nothing to do with being a monopoly. When big companies do shitty things to undermine normal competitive forces they get scrutiny.
The former is absolutely true. The latter is absolutely not. Hence why the government is looking into it.
Apple's actions are completely inexcusable and borderline illegal. It is only by incredible bravado and arrogance that they could have ever thought that 3.3.1 would be acceptable. They could have accomplished the same goal more subtly, but, probably due to Jobs universe-sized ego, they had to bring this upon themselves.
"This is how the free market is supposed to work."
No, it isn't at all how the free market is supposed to work. 3.3.1 is the exact opposite of a free market.