This may actually be a good thing...and I can't believe I'm actually saying that about a Cloud Computing (tm) product...but roll with me for a minute; I think this may be a worthwhile system for them to be using...
1.) Onenote's first release was back in 2003. After over ten years of existence, plenty of people still don't know what it is. Onenote was originally intended to be the killer app for tablets (back when they all had pens and keyboards and were running Windows XP Tablet PC Edition...). Why not do whatever it takes to get it on Tablets?
2.) The Slashdot crowd cares a lot about privacy. Most computer users don't. Most computer users upload data to Dropbox and Google Drive without hesitation. The requirement of storing their data on Microsoft's mothership will likely be even less of a concern. If anything, users are more likely to be better served by a system that doesn't require them to be involved with file sync management hell, or worried about losing all their notes once "click of death" comes to a hard disk near them.
2b.) If privacy is of greater concern than one's money, it's possible to buy Office 2013 outright, or hit The Pirate Bay. The fact that there is a free cloud-only option, thankfully, did not preclude Microsoft from selling the locally saving flavor.
2c.) I haven't tested this, but I do wonder if it's possible to download one's OneNote notebook from the OneDrive once it's stored there...it seems logical for the two-step method to work...
3.) Onenote can really shine with the collaboration and seamless syncing. If Microsoft does it right, I think it will give them some good PR to have a Onenote notebook seamlessly work between a user's iPhone, Android tablet, Windows laptop, and web browser. I think that, if there were any particular program that lent itself to a cloud sync method of replication, it's OneNote - Unlike Word and Powerpoint, which use self contained document files, Onenote is more like Outlook in that notebooks are more database/PST-like single mammoth files. Sharing individual pages via The Cloud (tm) will be much easier than some sort of import/export version hell. All of this together, I think, makes Onenote more useful than just "a five subject notebook on a computer".
4.) Microsoft's other gain here is (potentially) an uptick in people actually using their whole Microsoft account - OneDrive, Outlook.com, and Office Web Apps. If Onenote is free in exchange for also using those other services, then I think that this method of "enticing users to get a Microsoft account" is less objectionable than their method of "enticing users to use the Metro UI". Even if a user never uses a single Microsoft property besides Onenote, they still get 7GB of storage...and a 7GB Onenote notebook is a rather large piece of data...
Bonus point: Google requires a Gmail account in order to use QuickOffice, even if you intend on storing a document locally. It's bad when they do it as well, I'm just saying that there's precedent for an application to still require login and that it wasn't Microsoft who started this trend.
All in all, as much as I hate storing things in The Cloud (tm), I think that the benefits for most people make it less objectionable for the masses than it is for us Slashdot folk.