I think there are two things here.
First : Ubuntu is and will remain free. At least, that's what they claim.
This should answer some of your concerns.
Then there is Canonical. This company is a for-profit company, supposed to make money by contributing/supporting Ubuntu. Since Ubuntu is free, they obviously need to find other means of making money. And this is where the problem lies : in order to make money, they plan to add new services/features that will not be part of Ubuntu, but sold alongside it.
Ubuntu One is an example.
What is debated here is their way to achive that : by forcing evey contributor to give up their freedom in licencing model, and let canonical "own" everything contributed. This giving up of freedom is an ethical problem. It goes against the "mind" of the free software licences. And could break the free spirit of Ubuntu itself.
I think the main issue is a question that we can't answer now: how much of Ubuntu will stay "free" as it is claimed, and how much will be optional services sold by canonical ?
If more and more "super-features" are being added as paying options, you could argue that Ubuntu is less free than it should... Especially if those features are proprietary software (lacking even the "free-as-in-speach" side of the "free" meaning).
Right now, I think Canonical is still doing its job, and I still appreciate it. Ubuntu is a really solid and user-oriented distribution, and I won't change because of this article. But that's a personal statement, and since I'm not a defenser of the free software, it cannot be seen as "the" answer to the question.
Moreover, I really don't have a crystal ball to look at the future :-) In some years from now, maybe I will change my mind and start using something else because Canonical has been pushing too far their commitment for profitability... I really hope that's not going to be the case.