Esse é o comportamento pretendido no Passenger.
Veja aqui :
A Rails application is started as the owner of the file config/environment.rb, and a Rack application is started as the owner of the file config.ru. So if /home/webapps/foo/config/environment.rb is owned by joe, then Phusion Passenger will launch the corresponding Rails application as joe as well.
Para parar esse comportamento e ter o apache
stick, defina PassengerUserSwitching off
.