It speaks volumes that the most popular post on this blog is Missing the root.disk. It has nearly double the hits to the next most popular post (that also relates to Wubi boot problems).
What does this mean: to be missing the root.disk?
Well it's the catastrophic failure of Wubi, the damage and possible destruction of the virtual disk, in other words, the entire Ubuntu operating system and data. There really can't be much worse of a failure.
What is the cause?
It could be the forced shutdown of the computer, for example, due to a system freeze. In some cases, users reported a crash. In other cases, they reported nothing more than running available updates. It's not conclusive what the main cause is.
Why do people force shutdown?
There are probably many reasons this happens... like any bug that causes a system freeze. E.g. on my 12.04 Ubuntu install when I come back from suspend the screen sometimes remains black (mouse still visible). This isn't a freeze but there is no obvious way to shutdown or restart and no apparent fix/workaround. It would be totally understandable that some people might force shutdown if that happened to them. Especially coming from a Windows background where there is no alternative to REISUB. In fact, on my test Windows 8 install it freezes frequently and - as far as I know - that's my only option to reset.
So usability bugs like that could also be behind the corruption.
PS For this particular bug, I generally Ctrl+Alt+F1 and restart the lightdm desktop service (but it still kills all open apps).
Why does a forced shutdown corrupt the ext4 and/or ntfs file system?
This is perhaps the more relevant question. Maybe the journalling built into ext4 leads to corruption (speed over stability?). But this is pure speculation - and I thought Wubi installs were supposed to automatically sync all changes, precisely to avoid this problem.
And why would this affect the root.disk, a fixed-size file on NTFS...why does Wubi even update anything that could lead to this fixed file becoming corrupt? This seems like a major flaw.
How unstable is Wubi?
It's not possible to answer this without understanding how many people use Wubi and how many of those experience corruption of the root.disk. The fact is that I have never lost a root.disk to corruption in multiple years of testing Wubi, and over a year of continual use of Wubi (running the development releases)... so while I can't definitively say what is going on, I don't believe it's that unstable.
Regardless, the fact is, it shouldn't happen to anyone, and clearly it happens to many.
Why do people use Wubi?
I get that Wubi is a great way to try out Ubuntu without partitioning. It runs extremely close to a normal dual boot, that it showcases Ubuntu for those that are understandably nervous about partitioning. That makes sense. But why do they people keep on using it? Probably because it works too well. There isn't a whole lot of understanding about why it's not a great idea to do all your university coursework on a Wubi install and not bother to back it up. There also isn't any notification or warning when you install Wubi from here that there could be problems ahead or even an explanation of how Wubi is different unless you follow the links. In short, there's no reason for a user to switch to a partitioned install (usually until a major failure and the resulting investigation).
What do I think about Wubi?
I think it's pretty amazing to try out Ubuntu, but that it's poorly supported: I don't believe there is a credible maintenance and testing infrastructure for Wubi. If there were then you would see some effort to resolve these sorts of issues. And from experience I can assure you that getting even well-understood, major Wubi issues resolved (even when the fix is known), can be like pushing a rope.
Having said that, 12.04 is probably the most stable Wubi release ever - there's a huge drop in support requests. So it's working better than ever before and it seems to be popular and part of Canonical's strategy to spread Ubuntu.
I touched on the fact that I don't believe there is a credible maintenance plan in place for Wubi. My impression is that, in general, Canonical's resources are stretched too thin. There are many important, unresolved issues with Ubuntu at any point in time, and Wubi's issues are obviously not high on that list. I've been using 12.04 since it's release and I've found a number of usability bugs that make it a frustrating experience. On top of that, the seemingly small Ubuntu developer team are always fully occupied, working hard to produce these relentless 6 month releases, which I believe is far too frequent. All that time spent on a development release for zero production users is time taken away from millions of real production users. This doesn't make any sense to me whatsoever. It should be the other way around. Because of this endless cycle of less than perfect releases and not fixing existing problems they are slowly going to whittle away at the support base and scare off newcomers. So... in short I believe the Wubi maintenance issues are minor compared to the general maintenance issues.