Don't think the author has updated this recently. But I have this working with OmniFocus 2 (on Yosemite beta 3).
The issue is that the OmniFocus cache has moved in OF2. So, here's what you can do to patch things up ...
NOTE: Assuming you have downloaded the latest (from December 27 2013) version of the workflow and installed it.
1) Open Alfred options, and find the OmniFocus workflow.
2) Double Click the central .of script action
3) At the bottom right of the action's pane, there is a button titled "Open workflow folder". Click that.
4) Edit the file ofHandler.sh
5) Near the top of the file, there is a getOFCacheDir() shell function. You need to edit the path in that function as follows ...
If your OF2 app came from Omni's web site, use this ...
local OFCD="${HOME}/Library/Containers/com.omnigroup.OmniFocus2/Data/Library/Caches/com.omnigroup.OmniFocus2"
If your OF2 app came from the Mac App Store, use this ...
local OFCD="${HOME}/Library/Containers/com.omnigroup.OmniFocus2.MacAppStore/Data/Library/Caches/com.omnigroup.OmniFocus2.MacAppStore"
Save the edited file. Restart Alfred.app. And you should be in business.
NOTE: I did this with the Mac app store version. Haven't tested the direct from Omni version. I guessed that path using info from the OmniFocus forums. If it doesn't work, suggest you browse your filesystem in that area starting with ~/Library/Containers and you should find it.
-Cheers