I just recently started learning RoR. In Rails by default available Prototype. Why uses it is this library? Why is not jQuery, Dojo, Mootools, ExtJS ...
It was a choice made about five years ago, and was basically just the favorite JS framework of DHH at the time. Rails 3 will support switching that easier, but for rails 2, you can always just use http://github.com/aaronchi/jrails to swap in jquery for prototype.
As Matt Briggs mentions, prototype was state-of-the-art 5 years ago.
TBH, it's been a very long time since I used the built in javascript helpers. I write my apps using unobtrusive JS techniques with jQuery rather than the defaults. All you need to do is delete the default files and include whatever library you want in your layout.
Rails 3 changes this limitation, btw by adding hooks for unobtrusive JS with any library.
If I recall correctly from the Prototype & Scriptaculous book, it was originally part of Rails and is now a spin-off. The point was to make JavaScript look and act more like Ruby.
At the time of the writing Prototype wasn't just the state of the art, it was THE library to use. However if you just use javascript_tag to require jquer - it will work just fine, except to your rjs helpers. However that i changing in Rails 3 thanks to Merb influence and Yehuda Katz in particular ( one, but not the only one, of the Rails 3 Core, Merb and jQuery core members)