In an ideal world, software vendors would write native ports of their applications for Linux and release the source under the GPL. But that's never going to happen, even if Linux gains more market share. After all, Apple currently commands about 10% of the desktop market, yet many closed-source developers have yet to port their products, including most modern games, to OS X.
While Ubuntu should stay true to the goal of encouraging the use of free, open-source software wherever possible, it should not close its doors on Wine and winelib as a means of smoothing over the obstacles that prevent many Windows users from switching to Linux--and, more importantly, that discourage developers from writing applications for free platforms.
Porting, maintaining and supporting many applications to run natively on Linux involves a huge amount of work, especially when they're written in languages that don't lend themselves to cross-platform operability. Compiling code against winelib in order to ensure compatibility with Wine, on the other hand, is often much easier. It's also a convenient way of releasing software for Linux without having to make the source public, which many developers are reluctant to do.
I realize that calling for widespread adoption of closed-source Windows applications on Linux is pretty heretical, and I fully expect to face the unmerciful wrath of the GNU stalwarts in the audience. I'd like to stress first, however, that I like freedom and free software a lot, and believe in the ideology upon which open-source code is built. But at the same time, I like having a computer that lets me do as much as possible as easily as possible. Having more Windows applications available via Wine would go a long way towards making the Ubuntu experience the best it can be.
In defense of moderationUbuntu should continue to encourage the development and use of free, open-source, native applications for Linux. It should not be reluctant to work with developers who want to make their products available on Ubuntu via Wine.
Dismissing Wine as a distraction from the ultimate objective of a 100% free and open-source computing experience is radical and unrealistic. Traditionally, Shuttleworth and Ubuntu's developers have stood out as reassuring centers of moderation and pragmatism in a software ecosystem dominated by bombastic extremists. Let's hope they have the wisdom to extend their Realpolitik to Wine as well.