I don't have any problem with such configuration: CocoaPods 0.28.0 and Xcode5 (+ Command-Line Tools) here and building using the Command-Line quite often (especially for Continuous Integration) without having any problem.
- Neither with the Apple's
xcodebuild command, nor with xctool (see also this NSHipster's article) when building my personnal project using Travis-CI either, everything works fine;
- At work we have plenty of Xcode workspaces created using CocoaPods /
pod install and we use Jenkins-CI to run xcodebuild to build them and no problem either.
Maybe you need to check a bit more about your configuration? Which CocoaPods & Xcode version, Which Command-Line Tools (xcode-select --print-path?), How is you Xcode configured (maybe you changed some of Xcode's default settings that broke it somehow)?
Tell us more about your specific configuration and the error/warning messages you got, because there should not be any problem.
Also make sure you have an up-to-date version of CocoaPods (some stuff were fixed some versions ago regarding Xcode5 and the new arm64 architecture, that broke implicit dependency detection in some cases)