There could be a couple reasons for this. First off, and the easiest, is simply that your web browser, running under your normal user account, won't allow you permission to alter much of anything outside of your home directory. More likely however, is simply that your user (again, the one who calls the browser), doesn't have admin priviledges to your web application software.
Most software allows you the option to switch into administrator mode, but as a safety precaution, some software also allows you the ability to turn off this option, thereby preventing anyone else from attempting brute-force attacks through a browser, local or otherwise. If the ability to run in your web app's administrator mode is disabled, you aren't going to be able to do so, regardless of what user you are when you start the browser.
Typically, this option is in a config file, usually a text file in either /etc/ or whatever directory the program is installed into. As usual, check the docs on the project's homepage if they are available, especially the install documentation (even if you installed it as a binary package through your distribution, because occasionally mistakes happen).
If that fails, post an addition to this thread, or start another (if you don't get a response in a day or two), and include the name of the web app you are trying to use. Without the name of the program you are trying to run, it's kind of guesswork. (Reread your post, pretending to not know what software you are using, and you'll understand.)