Yesterday (3/10/14) when iOS 7.1 was released I also upgraded to Xcode 5.1 and found that my PhoneGap/Cordova project would no longer compile to my iPhone 5s. I also upgrade
@Shazron posted the fix on the Apache JIRA - he notes that the fix will be released as part of Cordova 3.5:
Here's a link to Shazron's complete writeup of this problem: http://shazronatadobe.wordpress.com/2014/03/12/xcode-5-1-and-cordova-ios/
It is now released and the short version of what to do is:
Cordova CLI 3.4.1-0.1.0 is out, which includes Cordova iOS 3.4.1 which incorporates all the fixes mentioned in this blog post. Update your Cordova CLI, and if you have an existing project, do a “cordova platform update ios“.