I was also having the same problem starting today, initially only on my 1st Gen iPhone, but then on my Mac with a MobileMe account.
I did get it working, though I changed so many things at once and had little problems to fix along the way, I can't really describe it in detail. But what seemed to have an effect is to go to WebDav and change the URL from using https to http. The URL is
http://idisk.me.com/username/Documents.
I can't say this is what fixes it, but I feel like that's what worked for me.
What confused my testing is when I configured OmniFocus on the iPhone to go with WebDav, it kept switching itself back to iDisk. Somehow I got it to stick eventually, but my poor testing methodology left me without much idea of what.