The home page for Prototype is prototype.conio.net. This site contains almost nothing other than the Prototype code itself; not even documentation is located here. A reference guide to Prototype is at www.sergiopereira.com/articles/prototype.js.html, and it's a good starting point for experienced JavaScript and Ajax programmers.
The following URLs contain additional tutorials, hints and references for Prototype: www.sitepoint.com/article/painless-javascript-prototype, blogs.ebusiness-apps.com/jordan/pages/Prototype%20Library%20Info.htm, particletree.com/features/quick-guide-to-prototype and wiki.script.aculo.us/scriptaculous/show/Prototype
Some people have argued that Prototype causes more problems than it is worth, discouraging thoughtful use of JavaScript. For one such perspective, you can read James McParlane's article at blog.metawrap.com/blog/WhyIDontUseThePrototypejsJavaScriptLibrary.aspx.
Finally, for more information about JavaScript, I recommend David Flanagan's JavaScript: The Definitive Guide, published by O'Reilly and now in its fifth edition. My favorite Ajax book continues to be Ajax Design Patterns, also published by O'Reilly and written by Michael Mahemoff.