As the error message indicates, it's complaining that it cannot access
/usr/local/lib/ruby/gems/1.8/gems/passenger-3.0.0/agents/PassengerWatchdog
because of a permission problem. You need to fix that.
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You need to check *all* parent directories as well. Each one of them
must be executable by the web server process.
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The only thing left that I can think of is SELinux interfering. Try
turning it off or setting it to permissive mode.
I know little about writing SELinux policies, so if anybody can
contribute and maintain a policy file that would be great.