It depends on what you want to distribute.
If your application is an AIR application, it can be downloaded and installed, installed from the web without downloading, or provided via CD or DVD and installed.
If your application is a Flex application, it is usually hosted on a web server, and wrapped in an HTML file, so the user just accesses the URL of the HTML wrapper file to access your application, then they can login if you have built in such functionality or just use your app if no login is required.
You could even build a Flex app to deliver other programs, like C++, Java, or other applications. In that case your app would simply be the delivery method, and once again it would be accessed via the HTML wrapper file.
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