Prototype is a good library. As are Dojo, Yahoo, Moo and Mochikit. Often companies don't have time to fully evaluate so many choices so they go with what they know, what suits their style, or what is prebundled with their back-end choice. The web is big enough for all these libraries to succeed.
Mike
Are there any standard arguments for Prototype that I don't know about? Or is it simply a matter of preference and that's all? Just curious.