The main reason is that, with Apple, you never know. If the AppStore is a huge success, which it most certainly will be, there may come the day where it will become the only real source for Mac programms, with Apple as the censor above them all. And imo this is a really bad thing, because who is Apple to know what everybody wants on ones own computer, bought with ones own money?
This completely closed platform thing works great for mobile phones, but not for much more complex computers.
Apart from that, Apple will collect the data from everyone who ones a Mac and uses the AppStore. Profiles of what people like, what they don't like, what they download and what they use for how long. There will be buyers for that, be it other corporations or the government. And the way it works with deals between big corporations and governments, you won't even know about your data being sold to the highest bidder.
So, you can call me paranoid, which many of you will, but anybody can inform himself about some really bad things going on on the internet censorship/surveillance front. So if I see something that provides infrastructure for this, and I don't really see any actual benefit for me, it's an easy choice not to use it.
While I absolutely like my Mac Pro, my MacBook Pro and Mac OS 10.6., I don't have to like every single one of Apples offerings. I don't have an iTunes account either, as I'm oldfashioned and prefer to buy CDs.