Hey @MikeJanik - I just restarted XCode and tried it again and was able to move past this issue. Then I started to get a security issue and the following answer helped me because I finally got the profile in General > Settings.
@rkleim Hi, I imagine the F.lux_team are a little busy right now trying to clean out the 'black screen' issue so, having had a similar experience to you initially I though I may be able to help.
I have made up a couple of screen caps that may explain.
I am assuming that you have successfully loaded the “iflux.xcodeproj” project in Xcode. The next step relates to the 'XCode/Preferences...' menu item, that is the preferences for XCode not this particular project. Shortcut: ⌘ , You will see this screen: http://imgur.com/72NxASQ
Click on the 'Accounts' tab and enter your Apple (iCloud) ID.
Then go to the main XCode screen with the f.lux project loaded and in the centre make the adjustments indicated here: http://imgur.com/34V96w2
Then with your iOS device connected, press ⌘R follow the bouncing ball.
I hope this helps. I'm sure I will be corrected if I have said anything incorrect.