I'm having the exact same problem -- I can't sync to my iPhone because our WebDAV server uses a self-signed SSL certificate, and OmniFocus on the iPhone just says 'untrusted SSL certificate'. This is such an obvious failure mode, I can't believe there's not simply the option in the dialog for OmniFocus to trust the certificate. The capitalization in the dialog box isn't even correct and the error message is so terse that it was obviously an after-thought and nobody even considered the fact that people might need to trust an untrusted certificate. And users shouldn't have to install untrusted certificates via the iPhone Configuration Utility, even if that worked.
I just spent $79.95 on OmniFocus because it can finally sync to the iPhone, and then another $19.99 for the iPhone app itself. This makes me really ticked off -- I just spent $100 on all this for the express purpose of having access to everything on my iPhone, and it doesn't even work. I feel like I shouldn't be writing such an antagonistic post, because this is the first release of the iPhone software and obviously your engineering man-hours are limited. But on the other hand, every feature you add to the app should be properly implemented -- it doesn't do anyone any good to cram a whole bunch of features into something if they're all half-assed. A hundred dollars is a LOT of money for a piece of software.
And you can't ask people to sync over HTTP -- I have sensitive information in OmniFocus, not my grocery list. After spending $100 I'm now supposed to go out and spend $500 on an SSL certificate because OmniFocus can't give me the simple option of trusting my own certificate? Arrrggghh.
Do you have an idea when this will be fixed?