The usual reasons are:
- Its good SEO practice, ensuring content is parsed and linked properly by search engines
- Some modern web enabled phones do not process client side script properly
- 508 compliance, in addition to helping SEO, is to some degree required by most government projects
- Some people just turn it off for whatever reason
The general rule is to provide enhanced functionality but degrade gracefully for those that cannot use the enhanced feature set. That means all navigation should be accessible without scripting, as well as all content for search engine parsing.
Think of SO. Questions and answers are processed server side and sent to the browser. Until recently comments were retrieved on demand through javascript to a web service call. That means that no matter how great a comment was, it is not going to be parsed by a search engine.
