The ~/.profile script is only meant to be read by your (presumably POSIX compatible) shell. And even then only if it is what is known as a "login" shell. For example, from the bash man page:
When invoked as an interactive login shell, or a non-interactive shell with the --login option, it first attempts to read and execute commands from /etc/profile and ~/.profile, in that order.
If you're running your rails application from an interactive shell prompt it should have access to the env vars you're setting in ~/.profile. If you're starting your rails app some other way (e.g., from your window manager) then you'll need to find some other way to set the env vars that it inherits.