You can add jQuery to your Rails project like you could to any server technology. The reason people say rails and proto/script go together is in Rails you can write 'RJS' templates which is ruby code that gets compiled into proto/script javascript code, allowing you to add javascript effects to your page without learning javascript. As such, proto/script comes bundled with rails.
Here was an article that was influential to me picking jQuery: http://jquery.com/blog/2006/08/20/why-jquerys-philosophy-is-better/ Its been awhile since I've used proto/script, and I'm sure its made a ton of progress, but once you go jQuery, you never go back ;)
