Yeah, the WMA format allows for far more customizeable control over how the files are licensed. It's what allows them to have the files expire if you cancel the service, etc.
A better question is becoming, why doesn't Apple just enable WMA support on iPods (I've read that their processors do have the codec). But, as has been Apple's downfall in the past, they're choosing proprietary exclusivity over open shareability. The theory being that if they convince everyone they're player is the gold standard, then they have no reason to play nice.
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-TJ
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