You really can’t. An .htaccess file allows you to set server directives, so you could use it to restrict files or folders, but you’d need to add each user to it, either manually or through a script. You’d also need to create and maintain passwords for those users. All that would do is allow them access to a particular folder, it wouldn’t create folders for each user.
What exactly are you trying to do? What will your app do? How much have you done so far? What will a user see when they visit http://www.yourdomain.com/username?
The more information you can provide about what you’re trying to accomplish, the easier (and thus, more likely) it will be for someone to prescribe a solution.
Also, the codeigniter user guide is VERY thorough, it provides you with enough information to do what you’re trying to do. So if you’re asking for help with things that are already in the user guide, you’re really just wasting time.