I'm in a development environment and we're using basic .htaccess/.htpasswd authentication to keep lurkers out. But some of my AJAX calls are coming back with HTTP/401 authentication failed errors. Is it possible for me to allow access only to those specific URL's? I can't easily do it by popping a new .htaccess in a subfolder because CodeIgniter uses ReWrites.
It's not possible to allow access only to those specific URL's. Unfortunately, .htaccess and .htpasswd authentication operates on a directory level only. And you're exactly right about why just using a subdirectory won't work - b/c of CI rewrites, which happen AFTER Apache has transferred control to CodeIgniter's index.php front controller.
The easy option, if you're working on something that (1) is not likely to be hacked in the first place, and (2) can't reveal sensitive data even if it is, is to use security via obscurity. Don't have any links to your dev site, include a noindex directive for search engine crawlers, and go on your merry way. This also has the advantage that you can test versions of the site with your colleagues and friends by just telling them the URL to go to.
If you're more worried about security, then you're probably building an auth module for your website's users. In that case, for your dev environment, just call that auth module in the constructor for all of your controllers, and redirect to the login page if the user is not logged in.
Good luck!