I believe it's to do with the way that they account for the revenue from the iPhone vs. the iPod touch. I'm not too sure about the details, but they can't add new features to existing products without charging and upgrade fee or else they'd be breaking some law or defrauding the shareholders or something. For the iPhone they account for the initial fee as being a "subscription" over two years, so they can provide free software updates within that period legally. Or something along those lines. I would guess that after two years, they would have to charge for updates to the iPhone too.
It's the same reason as they had to charge $1.99 for the utility that enabled 802.11n on the early MacBooks Pros.

Yes, it's stupid. But I don't think there's anything they can do about it. Maybe they should have adopted the same accounting model for the iPod touch as the iPhone. But, of course, there might have been a good reason why they didn't... I'm no business law expert, so I couldn't say.

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You actually believe that a company is forced by law to ask money for software updates?

I beg your pardon...

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"It’s an accounting requirement that if you upgrade a device that’s not on a subscription, you have to charge," Needham and Company financial analyst Charles Wolf said. "Apple has a choice of what to charge, but they have to charge."

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