Outside of geekdom people like us, I'm not sure there actually is confusion about Surface not running regular Windows programs, at least that has been my experience so far.
Plenty of people at my office (we have over 500 non technical employees at my place of work) have seen me using my surface in the breakroom and had a play. So far every single person who has looked at it gets that it's essentially a Microsoft iPad and doesn't run regular Windows apps. When I point out that it also runs full office then they regard that as a bonus.
Not one employee so far has expressed disappointment that the surface can't run regular apps. In fact, I know of at least 4 people who have played with my surface who then went out and bought one. I've even had employees I don't really know too well track me down because they've heard about surface and the fact that I have one and they want to have a play. In all my time here I don't think that has ever happened for a Microsoft product before. There genuinely does seem to be excitement among at least some of the general populous for surface that I haven't seen in a long time.
Of course, this is a very small sample size of people, but it makes me think that mostly the issue of not running regular programs is one that gets tech bloggers and technical people worked up way more than it does regular users.
Ah, come on. With a bit creative thinking (instead of political thinking, what MS did) you still could get the best of both worlds. How about a "professional mode" on WinRT devices: They can't run Win32 except for Office, but, you could unlock the ability - with huge scary "at your own risk" banners if needed.
Bang. You would have a kick-a$$ device for the absolute beginners, and for the pros. Problem solved.
Win8 could be great, yet MS took the most anal way with it possible, with every decision.
But we already pretty much have that (or will have). It's a surface pro or any other i386 tablet/touchscreen laptop.
A further issue standing in the way of having a desktop app unlock feature for regular surface is that it wouldn't be that easy - the regular windows apps would have to be compiled specifically for Arm. (We've had this mess before with Pocket PC and old style Windows phone - and believe me, as a former developer on those platforms I definitely don't want to have to go back to that again - building and testing one app for three different architectures was a giant pile of poo.
I think users would be more confused as to why their Windows copy of Photoshop won't run on their newly unlocked regular surface, rather than why their surface doesn't allow regular programs to work on it, at least based on my experience above...