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What are you running for system software on the iPhone? That link (which is not incorrectly coded, btw) works just fine on my old iPod touch (2G) running iOS 4.2.1, and when OF launches after the link being tapped, I get a screen warning that I have tapped on an OmniFocus settings link, do I wish to replace the synchronization settings? The format of the link was changed in OF 1.8 to be compatible with iOS 3.x and beyond.

It isn't particularly difficult to configure the OSS on the iPhone by hand. In 1.10 there will be even simpler setup for the OSS, but in 1.9, here's what you do:
  1. Go to the settings page
  2. Tap on the first entry under Sync (probably Nothing)
  3. Tap on Advanced (WebDAV)
  4. Fill location field with
  5. Go back to the settings page and tap Done
  6. You'll be prompted for Omni Sync user name (already filled in for you) and password