How can I protect a ClickOnce deployed application with a password? Do I have to change the IIS settings of the web or is there a way to do it programmatically?
I found a possible solution by myself in this MSDN article: ClickOnce Deployment and Security.
If you want to control which deployments each user can access, you should not enable anonymous access to ClickOnce applications deployed on a Web server. Rather, you would enable users access to the deployments you have installed based on a user's identity (using Windows NT authentication).
If you deploy to an environment without Windows NT authentication, a solution could be to try using ASP.NET form-based authentication to authenticate the user. However, ClickOnce does not support forms-based authentication because it uses persistent cookies; these present a security risk because they reside in the Internet Explorer cache and can be hacked. Therefore, if you are deploying ClickOnce applications, any authentication scenario besides Windows NT authentication is unsupported.
An additional security consideration occurs if you have to pass arguments into a ClickOnce application. ClickOnce enables developers to supply a query string to applications deployed over the Web. The query string takes the form of a series of name-value pairs at the end of the URL used to start the application:
http://servername.adatum.com/WindowsApp1.application?username=joeuser
By default, query-string arguments are disabled. To enable them, the attribute trustUrlParameters must be set in the application's deployment manifest. This value can be set from Visual Studio and from MageUI.exe. For detailed steps on how to enable passing query strings, see How to: Retrieve Query String Information in a ClickOnce Application.
You should never pass arguments retrieved through a query string to a database or to the command line without checking the arguments to make sure that they are safe. Unsafe arguments are ones that include database or command line escape characters that could allow a malicious user to manipulate your application into executing arbitrary commands.
Note: Query-string arguments are the only way to pass arguments to a ClickOnce application at startup. You cannot pass arguments to a ClickOnce application from the command line.