[eluser]TheFuzzy0ne[/eluser]
OK, now that makes much more sense.
.htaccess files are only read before the requested file. So the first .htaccess will work as expected, but after that, you're within the CI framework, and no further .htaccess files will be read. If you don't want a view/file to be accessible via your framework, then you need to code your app accordingly so it won't load it.