Also, there's more to the iOS story than the small amount of money that Apple makes from the app store. Apple has over $20 _billion_ in revenue per quarter from the iPhone [1], making Cydia's $10 million / year about a hundredth of a percent of Apple's revenue. Tim Bray has an interesting estimate [2] of how a small a fraction of iPhone revenue goes to software developers - $12 vs. $350 for the hardware - making Apple's cut an even smaller ~$5. I would argue that user experience and control are a much larger part of the motivation for locking down iOS than the additional revenue.
There's a good argument to made about the problems with closed platforms but, by being misleading about Apple's technology and motivation, the EFF does a poor job of making it here.
[1] http://images.apple.com/pr/pdf/q2fy12datasum.pdf [2] http://www.tbray.org/ongoing/When/201x/2012/03/04/Mobile-Mon...